{"gene":"TOMM6","run_date":"2026-04-28T21:42:59","timeline":{"discoveries":[{"year":1998,"finding":"Tom6 (yeast) functions as an assembly factor for Tom22, promoting its stable association with Tom40 within the ~400 kDa general import pore (GIP) complex of the outer mitochondrial membrane. In tom6Δ mitochondria, the Tom22–Tom40 interaction is destabilized, releasing Tom22 and generating a ~100 kDa subcomplex of Tom40, Tom7, and Tom5.","method":"Yeast genetics (tom6Δ mutant), Blue-native PAGE, co-immunoprecipitation, biochemical fractionation of mitochondrial outer membrane complexes","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 2 — reciprocal genetic/biochemical epistasis in multiple mutant backgrounds, replicated across labs","pmids":["9774667"],"is_preprint":false},{"year":1996,"finding":"Tom6 and Tom7 perform complementary and opposing functions in modulating TOM complex dynamics: Tom6 stabilizes the interaction between Tom22 and Tom40, whereas Tom7 exerts a destabilizing effect. Double-mutant (tom7Δ tom6Δ) synthetic growth defects provided genetic evidence for their functional relationship.","method":"Yeast genetics (single and double deletion mutants), co-immunoprecipitation, import assays with radiolabeled preproteins, in organello cross-linking","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods (genetics, biochemistry, import assays) in the foundational paper","pmids":["8641278"],"is_preprint":false},{"year":1999,"finding":"The TOM core complex of Neurospora crassa, consisting of Tom40, Tom22, Tom6, and Tom7, was isolated and shown to contain high-conductance channels forming two open pores (~2.1 nm diameter) as determined by electron tomography 3D reconstruction. The complex binds preproteins in a targeting sequence-dependent manner.","method":"Detergent solubilization/purification, electrophysiology (planar lipid bilayer), electron tomography, 3D reconstruction, preprotein-binding assays","journal":"The Journal of cell biology","confidence":"High","confidence_rationale":"Tier 1 — structural reconstruction combined with functional reconstitution","pmids":["10579717"],"is_preprint":false},{"year":2001,"finding":"During TOM complex assembly, Tom6 associates with the 100 kDa Tom40 intermediate (after Tom5 joins the 250 kDa intermediate), and maturation to the 400 kDa complex then occurs by association of Tom7 and Tom22. Tom6 thus acts at a specific sequential step in the assembly pathway.","method":"In vitro import assays with radiolabeled precursors, Blue-native PAGE, antibody-shift experiments, yeast mutant mitochondria","journal":"Nature structural biology","confidence":"High","confidence_rationale":"Tier 2 — sequential intermediates defined by multiple complementary methods","pmids":["11276259"],"is_preprint":false},{"year":2001,"finding":"In Neurospora crassa, Tom6 is in direct contact with Tom40 (shown by cross-linking) and interacts with Tom22 in a preprotein-dependent manner. The targeting and assembly information for Tom6 resides in its transmembrane segment and an adjacent N-terminal cytosolic flanking segment.","method":"Cross-linking, in vitro import/assembly assays, domain-swap hybrid constructs, competition assays","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods (cross-linking, domain mutagenesis, assembly competition)","pmids":["11278536"],"is_preprint":false},{"year":2001,"finding":"Tom40 and Tom22 together form the functional core unit of the GIP complex that stably retains preproteins; Tom6 (along with Tom5 and Tom7) is released under stringent detergent conditions while the preprotein remains, indicating Tom6 stabilizes the complex but is not the primary preprotein-binding component. The GIP complex exhibits two coupled channel activities corresponding to two simultaneously active Tom40 pores.","method":"Urea/alkaline resistance assays, detergent titration, electrophysiology (TOM channel activity), outer membrane vesicle import assays","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 1–2 — biochemical reconstitution with functional channel measurements and stringent controls","pmids":["11259583"],"is_preprint":false},{"year":2009,"finding":"Tom6 genetically interacts with SAM complex component Sam37: overexpression of Tom6 suppresses sam37Δ growth defects, and the double mutant (tom6Δ sam37Δ) is inviable. This suppression is linked to Tom6's capacity to stabilize the essential beta-barrel protein Tom40.","method":"Multicopy suppressor screen, yeast genetics (deletion mutants, double knockouts), growth assays, BN-PAGE","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 2 — genetic epistasis confirmed by biochemical stabilization assay","pmids":["19797086"],"is_preprint":false},{"year":2009,"finding":"The SAM complex forms two distinct large complexes with different functions in biogenesis of alpha-helical Tom proteins: a SAM-Tom5/Tom40 complex that binds the Tom6 precursor after Mim1-dependent insertion into the outer membrane, and a SAM-Mdm10 complex that handles Tom22. Tom6 assembly thus depends on prior Mim1-mediated membrane insertion.","method":"Co-immunoprecipitation, BN-PAGE, in vitro import assays, yeast deletion mutants","journal":"Journal of molecular biology","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods defining sequential pathway steps","pmids":["20026336"],"is_preprint":false},{"year":2010,"finding":"Tom6 plays a stimulatory role (opposite to Tom7's inhibitory role) at an early stage of Tom40 assembly at the SAM complex. Tom5 and Tom6 together promote formation of the mature TOM complex, while Tom7 antagonizes this process at two distinct assembly steps.","method":"In vitro assembly assays, BN-PAGE, yeast deletion mutants, co-immunoprecipitation","journal":"Journal of molecular biology","confidence":"High","confidence_rationale":"Tier 2 — genetic and biochemical dissection of multiple assembly steps","pmids":["21059357"],"is_preprint":false},{"year":2014,"finding":"The cytosolic precursor of Tom6 is phosphorylated by cyclin Clb3-activated Cdk1 during mitosis, enhancing import of Tom6 into mitochondria. Tom6 phosphorylation promotes assembly of Tom40 into the TOM complex and import of fusion proteins, thereby stimulating respiratory activity of mitochondria in a cell cycle-specific manner.","method":"Kinase assays (Cdk1 phosphorylation of Tom6 precursor in vitro and in vivo), phosphomimetic/phosphodeficient mutants, import assays, BN-PAGE, respiratory activity measurements","journal":"Science (New York, N.Y.)","confidence":"High","confidence_rationale":"Tier 1–2 — in vitro kinase assay plus mutagenesis and functional import/respiratory readouts","pmids":["25378463"],"is_preprint":false},{"year":2008,"finding":"Tom22, Tom7, Tom6, and Tom5 act as modulators of Tom40 pore dynamics: purified Tom40 alone shows gating only at high voltages, but the intact TOM core complex containing these small subunits significantly reduces the energy barrier between conformational states, enabling proper channel dynamics at physiological voltages.","method":"Planar lipid bilayer electrophysiology, single-channel recordings, purified TOM core complex vs. isolated Tom40","journal":"Biophysical journal","confidence":"High","confidence_rationale":"Tier 1 — direct electrophysiological comparison of intact complex vs. Tom40 alone","pmids":["18456827"],"is_preprint":false},{"year":2017,"finding":"Cryo-EM structure of the Neurospora crassa TOM core complex at ~10 Å shows a symmetrical dimer of ten membrane protein subunits. Tom6 (together with Tom5 and Tom7) surrounds each Tom40 beta-barrel pore as transmembrane alpha-helical subunits; Tom22 connects the two Tom40 pores at the dimer interface.","method":"Single-particle cryo-electron microscopy, 3D reconstruction","journal":"Cell","confidence":"High","confidence_rationale":"Tier 1 — cryo-EM structure with defined subunit assignments","pmids":["28802041"],"is_preprint":false},{"year":2020,"finding":"Atomic-resolution cryo-EM structure of the dimeric human TOM core complex (TOM-CC) shows that Tom6 (along with Tom5 and Tom7) surrounds the Tom40 beta-barrel channels in notable configurations. The complex has pronounced negative electrostatic features inside the channel and positive regions at the IMS periphery relevant to preprotein translocation.","method":"Single-particle cryo-EM, atomic model building","journal":"Cell discovery","confidence":"High","confidence_rationale":"Tier 1 — atomic-resolution structure of the human complex","pmids":["33083003"],"is_preprint":false},{"year":2008,"finding":"Human Tom5 and Tom6 were identified as components of the human TOM complex by immunoisolation of the TOM complex from HeLa cells expressing hTom22-FLAG followed by mass spectrometry. Human Tom6 is associated with Tom40. Knockdown of hTom40 decreases Tom6 levels; double knockdown of small Tom proteins (including Tom6) impairs preprotein import into the matrix.","method":"Immunoisolation (FLAG co-IP), mass spectrometry, siRNA knockdown, import assays, BN-PAGE","journal":"Biochemical and biophysical research communications","confidence":"High","confidence_rationale":"Tier 2 — identification confirmed by co-IP/MS plus functional knockdown with defined import readout","pmids":["18331822"],"is_preprint":false},{"year":2019,"finding":"Cell-cycle-dependent variation of phosphorylated Tom6 modulates the ratio of trimeric (Tom22-containing) to dimeric TOM complex: phosphorylated Tom6 promotes Tom22 integration into the trimeric TOM complex, and Por1 sequesters monomeric Tom22 that dissociates from the trimer, facilitating formation of the dimeric TOM complex preferred for import of TIM40/MIA-dependent proteins.","method":"Yeast genetics, co-immunoprecipitation, BN-PAGE, phosphomimetic/phosphodeficient Tom6 mutants, in vitro import assays","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods confirming phosphorylation-dependent complex switching","pmids":["30738703"],"is_preprint":false},{"year":2011,"finding":"Tom6 facilitates the mitochondrial localization of specific mRNAs encoding mitochondrial proteins: deletion of TOM6 (tom6Δ) caused mislocalization of OXA1 mRNA (but not ATP2 mRNA) from mitochondria in yeast, establishing a role for this outer membrane translocase subunit in mRNA targeting.","method":"Live-cell fluorescence imaging of endogenously expressed mRNA reporters, quantitative colocalization analysis in deletion mutant strains","journal":"RNA (New York, N.Y.)","confidence":"Medium","confidence_rationale":"Tier 3 — single localization assay in one deletion strain; no molecular mechanism for mRNA-Tom6 interaction established","pmids":["21705432"],"is_preprint":false},{"year":2025,"finding":"PP2A (with regulatory subunit Cdc55) dephosphorylates Ser16 of Tom6 in vitro. Synthetic trap-peptides mimicking phospho-Tom6 enriched PP2A and PP4 as full holoenzymes from yeast cytosolic fractions, with PP2A–Cdc55 identified as the first phosphatase of the TOM complex.","method":"Synthetic trap-peptide pulldown from yeast cytosol, mass spectrometry identification of phosphatases, in vitro dephosphorylation assay with purified PP2A","journal":"The FEBS journal","confidence":"High","confidence_rationale":"Tier 1–2 — in vitro dephosphorylation assay plus trap-peptide pulldown with MS identification","pmids":["40891445"],"is_preprint":false},{"year":2024,"finding":"Cryo-EM structure of the human TOM holo complex (~6 Å resolution) reveals a single Tom20 subunit positioned at the center of the complex, stabilized by extensive interactions with Tom22, Tom40, and Tom6. Tom6 thus contributes to docking the Tom20 receptor in the holo complex.","method":"Chemical cross-linking to stabilize Tom20, single-particle cryo-EM","journal":"PNAS nexus","confidence":"Medium","confidence_rationale":"Tier 1 — cryo-EM structure, but limited resolution (~6 Å) for precise side-chain contacts","pmids":["39071881"],"is_preprint":false},{"year":2025,"finding":"Cryo-EM structure of the Drosophila melanogaster TOM complex (3.3 Å) shows Tom6 assembled as an endogenous subunit surrounding the Tom40 beta-barrel, with the Drosophila TOM architecture very similar to the human complex but with small conformational differences at subunit interfaces attributable to variation in lipid-binding residues.","method":"Single-particle cryo-EM, 3.3 Å molecular model from ex vivo Drosophila retinal TOM complex","journal":"IUCrJ","confidence":"High","confidence_rationale":"Tier 1 — near-atomic resolution cryo-EM structure in an orthologous model organism","pmids":["39575538"],"is_preprint":false},{"year":2025,"finding":"In a mouse model of Alzheimer's disease, aggregated phospho-S670-GRK2 triggers aggregation of TOMM6 (human TOM6) and promotes mitochondrial dysfunction. Neuron-specific restoration of TOMM6 expression reduces beta-amyloid plaques but increases soluble beta-amyloid and mortality, indicating TOMM6 participates in mitochondrial quality control pathways relevant to neurodegeneration.","method":"Transgenic mouse models, Western blot for TOMM6 aggregation, neuron-specific TOMM6 overexpression, beta-amyloid quantification, survival analysis","journal":"Cell reports. Medicine","confidence":"Medium","confidence_rationale":"Tier 3 — in vivo loss/gain-of-function with defined phenotypic readouts but mechanistic link between TOMM6 and amyloid not fully resolved","pmids":["41895286"],"is_preprint":false},{"year":2025,"finding":"NF-κB directly upregulates TOM6 transcription during vascular calcification; TOM6 knockdown attenuates calcification while TOM6 overexpression exacerbates it. Mechanistically, elevated TOM6 impairs PINK1/Parkin-mediated mitophagy and mitochondrial bioenergetics. Luteolin binds IKKα/IKKβ to inhibit NF-κB, suppressing TOM6 transcription and restoring mitophagy.","method":"siRNA knockdown and overexpression in VSMCs, in vivo VitD3-overload and CKD rat/mouse models, RNA sequencing, molecular docking (luteolin-IKK binding), mitophagy assays, Western blot for PINK1/Parkin pathway","journal":"European journal of pharmacology","confidence":"Medium","confidence_rationale":"Tier 3 — in vitro/in vivo gain- and loss-of-function with pathway readouts, but mechanistic link between TOM6 import function and mitophagy inhibition not fully biochemically resolved","pmids":["41232657"],"is_preprint":false}],"current_model":"TOMM6 (Tom6) is a small alpha-helical transmembrane subunit of the mitochondrial outer membrane TOM core complex that stabilizes Tom22–Tom40 interaction during complex assembly; its import and assembly-promoting activity are directly regulated by reversible phosphorylation—Cdk1/cyclin phosphorylates Tom6's cytosolic precursor to enhance its mitochondrial import and TOM complex assembly in mitosis, while PP2A (with Cdc55 regulatory subunit) dephosphorylates Ser16 of Tom6 to reverse this effect—and structurally Tom6 surrounds the Tom40 beta-barrel channel in both yeast, fungal, insect, and human TOM complexes, where it also modulates channel gating dynamics and helps dock the Tom20 receptor in the holo complex."},"narrative":{"teleology":[{"year":1996,"claim":"Establishing the fundamental concept that Tom6 and Tom7 exert opposing regulatory effects on TOM complex stability resolved how small accessory subunits control the dynamics of a multisubunit translocase.","evidence":"Yeast single and double deletion mutants with co-immunoprecipitation, cross-linking, and radiolabeled preprotein import assays","pmids":["8641278"],"confidence":"High","gaps":["Molecular basis of the stabilizing vs. destabilizing mechanism not defined","No structural information on Tom6's position within the complex"]},{"year":1998,"claim":"Demonstrating that Tom6 specifically promotes the Tom22–Tom40 interaction within the ~400 kDa GIP complex pinpointed Tom6's biochemical target within the translocase.","evidence":"Blue-native PAGE and co-immunoprecipitation in yeast tom6Δ mitochondria","pmids":["9774667"],"confidence":"High","gaps":["Whether Tom6 contacts Tom22 directly or acts indirectly through Tom40 was unresolved"]},{"year":1999,"claim":"Isolation of the Neurospora TOM core complex (Tom40/22/6/7) and visualization of its twin-pore architecture established that Tom6 is an integral subunit of a functional channel capable of binding preproteins in a targeting-sequence-dependent manner.","evidence":"Detergent purification, planar lipid bilayer electrophysiology, and electron tomography 3D reconstruction","pmids":["10579717"],"confidence":"High","gaps":["Subunit-level resolution within the pore not achieved","Individual contribution of Tom6 to channel conductance unknown"]},{"year":2001,"claim":"Mapping Tom6's entry point in TOM complex assembly—joining the 100 kDa Tom40 intermediate after Tom5 and before Tom7/Tom22—defined a sequential maturation pathway and placed Tom6 as an early assembly factor.","evidence":"In vitro import of radiolabeled precursors, BN-PAGE, and antibody-shift assays in yeast mutant mitochondria","pmids":["11276259","11278536","11259583"],"confidence":"High","gaps":["Whether the same assembly order applies in mammalian cells was untested","The energetics driving each sequential step remained undefined"]},{"year":2008,"claim":"Two advances: (1) identification of human Tom6 as a bona fide component of the human TOM complex validated conservation from yeast, and (2) electrophysiology showed that Tom6 and other small subunits collectively modulate Tom40 channel gating dynamics at physiological voltages.","evidence":"Immunoisolation/MS from HeLa cells, siRNA knockdown import assays (human); planar lipid bilayer single-channel recordings comparing intact TOM core complex vs. isolated Tom40 (yeast/Neurospora)","pmids":["18331822","18456827"],"confidence":"High","gaps":["Individual contribution of Tom6 to gating vs. other small subunits not dissected","Structural basis of gating modulation unknown"]},{"year":2009,"claim":"Genetic interaction between Tom6 and the SAM complex (Sam37) and demonstration that the SAM–Tom5/Tom40 subcomplex receives the Tom6 precursor after Mim1-dependent membrane insertion defined the upstream biogenesis pathway for Tom6 itself.","evidence":"Multicopy suppressor screens, yeast double-deletion mutants, BN-PAGE, co-IP, and in vitro import assays","pmids":["19797086","20026336"],"confidence":"High","gaps":["How Mim1 recognizes the Tom6 transmembrane segment at a molecular level was unresolved"]},{"year":2014,"claim":"Discovery that Cdk1–cyclin B phosphorylates the cytosolic Tom6 precursor to stimulate its mitochondrial import during mitosis revealed a direct cell-cycle regulatory input into TOM complex biogenesis and mitochondrial respiratory capacity.","evidence":"In vitro and in vivo kinase assays, phosphomimetic/phosphodeficient mutants, import assays, BN-PAGE, respiratory measurements in yeast","pmids":["25378463"],"confidence":"High","gaps":["The identity of the phosphatase counteracting Cdk1 was unknown","Relevance to mammalian mitotic control not tested"]},{"year":2017,"claim":"The ~10 Å cryo-EM structure of the Neurospora TOM core complex placed Tom6 as a transmembrane helix surrounding the Tom40 β-barrel, providing the first subunit-resolved architecture of the translocase.","evidence":"Single-particle cryo-EM and 3D reconstruction","pmids":["28802041"],"confidence":"High","gaps":["Resolution insufficient for side-chain contacts","No structure of the holo complex with Tom20/Tom70 receptors"]},{"year":2019,"claim":"Phosphorylated Tom6 was shown to control the ratio of trimeric (Tom22-containing) to dimeric TOM complex, with Por1 sequestering released Tom22, thereby modulating substrate selectivity toward MIA-pathway clients—explaining how a single phosphorylation event rewires import specificity.","evidence":"BN-PAGE, co-IP, phosphomimetic Tom6 mutants, in vitro import assays in yeast","pmids":["30738703"],"confidence":"High","gaps":["Whether this trimer–dimer switching occurs in mammalian cells is unknown","Structural basis of Por1-mediated Tom22 sequestration undefined"]},{"year":2020,"claim":"Atomic-resolution cryo-EM of the human TOM core complex confirmed the conserved arrangement of Tom6 around Tom40 and revealed electrostatic features of the translocation channel relevant to preprotein passage.","evidence":"Single-particle cryo-EM with atomic model building","pmids":["33083003"],"confidence":"High","gaps":["Holo complex structure with receptors still missing at atomic resolution"]},{"year":2024,"claim":"A ~6 Å cryo-EM structure of the human TOM holo complex revealed that Tom6 participates in docking the Tom20 receptor, extending Tom6's role beyond core-complex stabilization to receptor organization.","evidence":"Chemical cross-linking stabilization of Tom20, single-particle cryo-EM","pmids":["39071881"],"confidence":"Medium","gaps":["Limited resolution prevents defining precise Tom6–Tom20 contacts","Functional consequences of disrupting this interface not tested"]},{"year":2025,"claim":"Three advances completed the picture: (1) PP2A–Cdc55 was identified as the phosphatase that dephosphorylates Tom6-Ser16, closing the kinase–phosphatase cycle; (2) the Drosophila TOM structure at 3.3 Å confirmed the conserved Tom6 architecture; (3) TOMM6 was linked to disease-relevant mitochondrial quality control—aggregation in Alzheimer's disease models and impairment of PINK1/Parkin mitophagy in vascular calcification.","evidence":"Trap-peptide pulldown/MS and in vitro dephosphorylation (PP2A); ex vivo cryo-EM from Drosophila retina; transgenic AD mouse model with TOMM6 overexpression; siRNA/overexpression in VSMCs with mitophagy assays","pmids":["40891445","39575538","41895286","41232657"],"confidence":"High","gaps":["Mechanistic link between TOM6 import function and mitophagy inhibition is biochemically unresolved","Whether TOMM6 aggregation in AD is causative or a downstream consequence is unclear","PP2A–Cdc55 as Tom6 phosphatase confirmed only in yeast; mammalian counterpart unknown"]},{"year":null,"claim":"Key open questions include: how Tom6 phosphorylation mechanistically switches TOM complex stoichiometry in mammalian cells; the structural basis of Tom6's role in modulating channel gating; and whether TOMM6-dependent mitophagy impairment represents a direct import-related mechanism or an indirect consequence of TOM complex remodeling.","evidence":"","pmids":[],"confidence":"Low","gaps":["No mammalian phospho-Tom6 functional studies","No high-resolution structure capturing Tom6 in the context of channel gating states","TOMM6–mitophagy link lacks reconstitution-level biochemical evidence"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0005198","term_label":"structural molecule activity","supporting_discovery_ids":[0,1,3,6,8,10]}],"localization":[{"term_id":"GO:0005739","term_label":"mitochondrion","supporting_discovery_ids":[0,2,4,11,12,13,18]}],"pathway":[{"term_id":"R-HSA-9609507","term_label":"Protein localization","supporting_discovery_ids":[0,3,5,9,13,14]},{"term_id":"R-HSA-1852241","term_label":"Organelle biogenesis and maintenance","supporting_discovery_ids":[3,7,8,9]},{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[0,3,9,14]}],"complexes":["TOM core complex (TOM-CC)","TOM holo complex"],"partners":["TOMM40","TOMM22","TOMM7","TOMM5","TOMM20","SAM37","MIM1"],"other_free_text":[]},"mechanistic_narrative":"TOMM6 is a small single-pass transmembrane subunit of the mitochondrial outer membrane TOM (translocase of the outer membrane) complex that stabilizes the Tom22–Tom40 interaction and promotes assembly of the mature ~400 kDa import pore, opposing the destabilizing activity of Tom7 [PMID:8641278, PMID:9774667]. Structurally, Tom6 wraps around the Tom40 β-barrel channel as a transmembrane α-helix in the dimeric TOM core complex across species and contributes to docking the Tom20 receptor in the holo complex [PMID:28802041, PMID:33083003, PMID:39071881]. The cytosolic precursor of Tom6 is phosphorylated by Cdk1–cyclin B during mitosis to stimulate its own mitochondrial import and enhance TOM complex assembly and respiratory capacity, and this phosphorylation is reversed by PP2A–Cdc55 on Ser16 [PMID:25378463, PMID:40891445]. Elevated TOMM6 expression impairs PINK1/Parkin-mediated mitophagy in vascular smooth muscle cells, and TOMM6 aggregation is linked to mitochondrial dysfunction in a mouse Alzheimer's disease model [PMID:41232657, PMID:41895286]."},"prefetch_data":{"uniprot":{"accession":"Q96B49","full_name":"Mitochondrial import receptor subunit TOM6 homolog","aliases":["Overexpressed breast tumor protein","Translocase of outer membrane 6 kDa subunit homolog"],"length_aa":74,"mass_kda":8.0,"function":"Component of the translocase of the outer membrane of mitochondria (TOM) complex essential for the recognition and translocation of cytosolically synthesized mitochondrial preproteins (PubMed:40080546). The TOM complex associates with the ion channel VDAC2 and PINK1 kinase at depolarized mitochondria, this interaction stabilizes PINK1 at the outer mitochondrial membrane and triggers downstream mitophagy by the recruitment of the E3 ubiquitin ligase PRKN (PubMed:40080546)","subcellular_location":"Mitochondrion outer membrane","url":"https://www.uniprot.org/uniprotkb/Q96B49/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/TOMM6","classification":"Not Classified","n_dependent_lines":22,"n_total_lines":1208,"dependency_fraction":0.018211920529801324},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/TOMM6","total_profiled":1310},"omim":[{"mim_id":"616169","title":"TRANSLOCASE OF OUTER MITOCHONDRIAL MEMBRANE 5; TOMM5","url":"https://www.omim.org/entry/616169"},{"mim_id":"616168","title":"TRANSLOCASE OF OUTER MITOCHONDRIAL MEMBRANE 6; TOMM6","url":"https://www.omim.org/entry/616168"},{"mim_id":"607980","title":"TRANSLOCASE OF OUTER MITOCHONDRIAL MEMBRANE 7; TOMM7","url":"https://www.omim.org/entry/607980"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Mitochondria","reliability":"Supported"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/TOMM6"},"hgnc":{"alias_symbol":["OBTP","Tom6"],"prev_symbol":[]},"alphafold":{"accession":"Q96B49","domains":[{"cath_id":"1.20.5","chopping":"30-62","consensus_level":"high","plddt":81.1133,"start":30,"end":62}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q96B49","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q96B49-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q96B49-F1-predicted_aligned_error_v6.png","plddt_mean":70.31},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=TOMM6","jax_strain_url":"https://www.jax.org/strain/search?query=TOMM6"},"sequence":{"accession":"Q96B49","fasta_url":"https://rest.uniprot.org/uniprotkb/Q96B49.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q96B49/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q96B49"}},"corpus_meta":[{"pmid":"9774667","id":"PMC_9774667","title":"Preprotein translocase of the outer mitochondrial membrane: molecular dissection and assembly of the general import pore complex.","date":"1998","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/9774667","citation_count":210,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"10579717","id":"PMC_10579717","title":"The TOM core complex: the general protein import pore of the outer membrane of mitochondria.","date":"1999","source":"The Journal of cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/10579717","citation_count":173,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"11276259","id":"PMC_11276259","title":"Multistep assembly of the protein import channel of the mitochondrial outer membrane.","date":"2001","source":"Nature structural biology","url":"https://pubmed.ncbi.nlm.nih.gov/11276259","citation_count":165,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"11259583","id":"PMC_11259583","title":"Protein import channel of the outer mitochondrial membrane: a highly stable Tom40-Tom22 core structure differentially interacts with preproteins, small tom proteins, and import receptors.","date":"2001","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/11259583","citation_count":145,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"28802041","id":"PMC_28802041","title":"Cryo-EM Structure of the TOM Core Complex from Neurospora crassa.","date":"2017","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/28802041","citation_count":141,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"11402060","id":"PMC_11402060","title":"Tom40, the pore-forming component of the protein-conducting TOM channel in the outer membrane of mitochondria.","date":"2001","source":"The Journal of cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/11402060","citation_count":140,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"8641278","id":"PMC_8641278","title":"Tom7 modulates the dynamics of the mitochondrial outer membrane translocase and plays a pathway-related role in protein import.","date":"1996","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/8641278","citation_count":137,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"25378463","id":"PMC_25378463","title":"Mitochondria. 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\"is_preprint\": false\n    },\n    {\n      \"year\": 1999,\n      \"finding\": \"Tom6 is a core component of the TOM core complex (alongside Tom40, Tom22, and Tom7) that mediates preprotein translocation across the outer mitochondrial membrane; the purified TOM core complex containing Tom6 exhibits high-conductance channels and binds preprotein in a targeting sequence-dependent manner.\",\n      \"method\": \"Detergent solubilization, purification of TOM core complex, electrophysiology in planar lipid bilayers, electron tomography\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — biochemical reconstitution with structural and functional validation\",\n      \"pmids\": [\"10579717\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1996,\n      \"finding\": \"Tom6 and Tom7 perform complementary and opposing functions in modulating TOM complex dynamics: Tom6 stabilizes receptor-pore interactions while Tom7 destabilizes them; genetic evidence from double mutants (tom7Δ tom6Δ) confirms their functional relationship.\",\n      \"method\": \"Yeast deletion genetics, synthetic lethality analysis, protein import assays\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — epistasis with clean KO and defined phenotype, replicated\",\n      \"pmids\": [\"8641278\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"Tom6 associates with the 100 kDa assembly intermediate of Tom40 during TOM complex biogenesis, and this association is required for maturation to the 400 kDa complex; Tom6 joins after Tom5 during the multistep assembly pathway.\",\n      \"method\": \"In vitro import assays, blue-native PAGE, pulse-chase assembly analysis in yeast\",\n      \"journal\": \"Nature structural biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — reconstitution-style in vitro assembly with mutant analysis, multiple orthogonal methods\",\n      \"pmids\": [\"11276259\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"In Neurospora crassa, Tom6 is in direct contact with Tom40 (cross-linking) and interacts with Tom22 in a preprotein-dependent manner; Tom6 precursor inserts into the outer membrane in vitro and assembles into authentic TOM complexes; the transmembrane segment and adjacent N-terminal cytosolic flank encode targeting and assembly information.\",\n      \"method\": \"Cross-linking, in vitro import/assembly assays, hybrid protein analysis\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — multiple orthogonal biochemical methods including mutagenesis-like domain swap analysis\",\n      \"pmids\": [\"11278536\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"Tom6 and Tom22 together with Tom40 form the stable core of the preprotein import channel; all three small Tom proteins (including Tom6) are released under stringent detergent conditions while Tom40-Tom22 retains accumulated preprotein, defining Tom40-Tom22 as the minimal functional unit.\",\n      \"method\": \"Urea/alkaline/detergent stability assays, outer membrane vesicle reconstitution, electrophysiology\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — multiple orthogonal biochemical dissection methods\",\n      \"pmids\": [\"11259583\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"Tom6 genetically interacts with Sam37 (the SAM complex subunit); overexpression of Tom6 suppresses sam37Δ growth defects by stabilizing newly synthesized Tom40; cells lacking both TOM6 and SAM37 are inviable, revealing a functional link between TOM assembly and the SAM pathway.\",\n      \"method\": \"Multicopy suppressor screen, yeast genetics, double-mutant lethality analysis, protein stability assays\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — epistasis by suppressor screen plus double-mutant lethality, functional mechanism defined\",\n      \"pmids\": [\"19797086\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"The SAM-Tom5/Tom40 subcomplex binds the precursor of Tom6 after Tom6 has been inserted into the outer membrane in an Mim1-dependent manner, revealing a sequential assembly pathway for alpha-helical TOM subunits involving two distinct large SAM complexes.\",\n      \"method\": \"Co-immunoprecipitation, blue-native PAGE, import assays with SAM complex mutants\",\n      \"journal\": \"Journal of molecular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal co-IP with defined pathway placement and multiple mutant backgrounds\",\n      \"pmids\": [\"20026336\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"Tom7 plays an antagonistic role to Tom5 and Tom6 at an early stage of Tom40 assembly at the SAM complex; Tom5 and Tom6 play stimulatory roles in formation of the mature TOM complex, while Tom7 inhibits at this same step.\",\n      \"method\": \"In vitro assembly assays, blue-native PAGE, co-immunoprecipitation with SAM complex components\",\n      \"journal\": \"Journal of molecular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — defined epistatic relationship between Tom6, Tom5, and Tom7 with multiple biochemical readouts\",\n      \"pmids\": [\"21059357\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"Cyclin-dependent kinase Cdk1 (activated by cyclin Clb3) phosphorylates the cytosolic precursor of Tom6 (yeast ortholog), enhancing its import into mitochondria during mitosis; Tom6 phosphorylation promotes assembly of Tom40 and import of fusion proteins, stimulating mitochondrial respiratory activity in a cell cycle-specific manner.\",\n      \"method\": \"In vitro kinase assay, phospho-site mutagenesis, import assays, respiratory activity measurement, cell cycle synchronization\",\n      \"journal\": \"Science (New York, N.Y.)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — in vitro kinase assay with mutagenesis plus multiple functional readouts, high-impact journal\",\n      \"pmids\": [\"25378463\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Cryo-EM structure of the TOM core complex shows that Tom6 (along with Tom5 and Tom7) surrounds the Tom40 β-barrel pore as α-helical transmembrane subunits in a symmetric dimer; Tom22 connects two Tom40 pores at the dimer interface.\",\n      \"method\": \"Single-particle cryo-electron microscopy at ~3.5 Å resolution\",\n      \"journal\": \"Cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — high-resolution cryo-EM structure with detailed subunit placement\",\n      \"pmids\": [\"28802041\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Cell-cycle-dependent variation of phosphorylated Tom6 modulates Tom22 dynamics: Tom6 phosphorylation causes monomeric Tom22 to be released and chaperoned by porin Por1, thereby regulating the equilibrium between the functional trimeric TOM complex and the dimeric form lacking Tom22.\",\n      \"method\": \"Co-immunoprecipitation, blue-native PAGE, cell-cycle synchronization assays, genetic analysis\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — mechanistic link between Tom6 phosphorylation state and TOM complex assembly established with multiple biochemical approaches\",\n      \"pmids\": [\"30738703\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Atomic cryo-EM structure of the dimeric human TOM core complex shows that Tom6 (TOMM6), Tom5, and Tom7 surround the Tom40 β-barrel channels; Tom6 adopts a notable configuration contributing to the electrostatic features of the complex relevant to preprotein translocation.\",\n      \"method\": \"Single-particle cryo-EM at near-atomic resolution\",\n      \"journal\": \"Cell discovery\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — atomic-resolution cryo-EM structure of the human complex\",\n      \"pmids\": [\"33083003\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"Tom6 (along with Tom22, Tom7, and Tom5) acts as a modulator of Tom40 pore dynamics, significantly reducing the energy barrier between different conformational states of the TOM channel; isolated Tom40 without these subunits shows reduced gating behavior.\",\n      \"method\": \"Planar lipid bilayer electrophysiology of purified TOM core complex vs. isolated Tom40\",\n      \"journal\": \"Biophysical journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1–2 — in vitro electrophysiology comparing complex vs. subunit, but Tom6 role not isolated individually\",\n      \"pmids\": [\"18456827\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"In the human TOM holo complex structure, Tom20 is stabilized by extensive interactions with Tom22, Tom40, and Tom6; cryo-EM reveals a single Tom20 subunit positioned at the center of the complex.\",\n      \"method\": \"Chemical cross-linking combined with single-particle cryo-EM (~6 Å resolution)\",\n      \"journal\": \"PNAS nexus\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 — cryo-EM structural data but moderate resolution limits detailed mechanistic interpretation of Tom6 contacts\",\n      \"pmids\": [\"39071881\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"PP2A (with regulatory subunit Cdc55) dephosphorylates Ser16 of Tom6 in vitro, identifying PP2A as the first phosphatase of the TOM complex; PP4 (with regulatory subunit Psy2) also interacts with Tom6. The interaction is mediated through the regulatory subunits of these phosphatase holoenzymes.\",\n      \"method\": \"Synthetic trap-peptide pulldown from yeast cytosolic fractions, mass spectrometry identification, in vitro phosphatase assay with recombinant PP2A on Tom6 Ser16\",\n      \"journal\": \"The FEBS journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — in vitro phosphatase assay with defined substrate site plus biochemical identification of phosphatase holoenzymes\",\n      \"pmids\": [\"40891445\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"In an Alzheimer disease context, aggregated phospho-S670-GRK2 triggers aggregation of TOMM6 and promotes mitochondrial dysfunction; neuron-specific TOMM6 overexpression reduces beta-amyloid plaques but enhances soluble beta-amyloid.\",\n      \"method\": \"Transgenic mouse models, co-aggregation analysis, neuron-specific TOMM6 expression rescue experiments\",\n      \"journal\": \"Cell reports. Medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 — defined functional consequence of TOMM6 perturbation in vivo but mechanistic link is indirect\",\n      \"pmids\": [\"41895286\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"NF-κB transcriptionally upregulates TOMM6 (human gene) during vascular calcification; TOMM6 knockdown attenuates calcification and promotes PINK1/Parkin-mediated mitophagy, while TOMM6 overexpression exacerbates calcification and impairs mitophagy.\",\n      \"method\": \"siRNA knockdown, overexpression, RNA sequencing, mitophagy assays, in vitro and in vivo vascular calcification models\",\n      \"journal\": \"European journal of pharmacology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 — functional loss-of-function/gain-of-function with defined pathway placement but single lab, single study\",\n      \"pmids\": [\"41232657\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Cryo-EM structure of the Drosophila TOM complex confirms that Tom6 is a core endogenous component co-assembled with Tom40, Tom22, Tom5, and Tom7; the overall architecture of Tom6 positioning is conserved between Drosophila and human TOM complexes.\",\n      \"method\": \"Single-particle cryo-EM at 3.3 Å resolution from ex vivo Drosophila retina\",\n      \"journal\": \"IUCrJ\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — high-resolution cryo-EM structure from an ortholog confirming conserved position\",\n      \"pmids\": [\"39575538\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"TOMM6 is a small α-helical transmembrane subunit of the TOM core complex at the outer mitochondrial membrane that functions primarily as a structural assembly factor: it stabilizes the Tom40–Tom22 interaction, associates with the 100 kDa Tom40 assembly intermediate to promote maturation to the 400 kDa GIP complex, modulates Tom40 channel gating dynamics, and undergoes cell-cycle-regulated phosphorylation by Cdk1 (dephosphorylated by PP2A via Ser16) that controls the rate of Tom6 import into mitochondria and thereby regulates TOM complex assembly and mitochondrial biogenesis in a cell-cycle-dependent manner.\"\n}\n```\n\n--- ROUND 2 (R2/R3, augmented corpus) ---\n\n```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 1998,\n      \"finding\": \"Tom6 (yeast) functions as an assembly factor for Tom22, promoting its stable association with Tom40 within the ~400 kDa general import pore (GIP) complex of the outer mitochondrial membrane. In tom6Δ mitochondria, the Tom22–Tom40 interaction is destabilized, releasing Tom22 and generating a ~100 kDa subcomplex of Tom40, Tom7, and Tom5.\",\n      \"method\": \"Yeast genetics (tom6Δ mutant), Blue-native PAGE, co-immunoprecipitation, biochemical fractionation of mitochondrial outer membrane complexes\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal genetic/biochemical epistasis in multiple mutant backgrounds, replicated across labs\",\n      \"pmids\": [\"9774667\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1996,\n      \"finding\": \"Tom6 and Tom7 perform complementary and opposing functions in modulating TOM complex dynamics: Tom6 stabilizes the interaction between Tom22 and Tom40, whereas Tom7 exerts a destabilizing effect. Double-mutant (tom7Δ tom6Δ) synthetic growth defects provided genetic evidence for their functional relationship.\",\n      \"method\": \"Yeast genetics (single and double deletion mutants), co-immunoprecipitation, import assays with radiolabeled preproteins, in organello cross-linking\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods (genetics, biochemistry, import assays) in the foundational paper\",\n      \"pmids\": [\"8641278\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1999,\n      \"finding\": \"The TOM core complex of Neurospora crassa, consisting of Tom40, Tom22, Tom6, and Tom7, was isolated and shown to contain high-conductance channels forming two open pores (~2.1 nm diameter) as determined by electron tomography 3D reconstruction. The complex binds preproteins in a targeting sequence-dependent manner.\",\n      \"method\": \"Detergent solubilization/purification, electrophysiology (planar lipid bilayer), electron tomography, 3D reconstruction, preprotein-binding assays\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — structural reconstruction combined with functional reconstitution\",\n      \"pmids\": [\"10579717\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"During TOM complex assembly, Tom6 associates with the 100 kDa Tom40 intermediate (after Tom5 joins the 250 kDa intermediate), and maturation to the 400 kDa complex then occurs by association of Tom7 and Tom22. Tom6 thus acts at a specific sequential step in the assembly pathway.\",\n      \"method\": \"In vitro import assays with radiolabeled precursors, Blue-native PAGE, antibody-shift experiments, yeast mutant mitochondria\",\n      \"journal\": \"Nature structural biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — sequential intermediates defined by multiple complementary methods\",\n      \"pmids\": [\"11276259\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"In Neurospora crassa, Tom6 is in direct contact with Tom40 (shown by cross-linking) and interacts with Tom22 in a preprotein-dependent manner. The targeting and assembly information for Tom6 resides in its transmembrane segment and an adjacent N-terminal cytosolic flanking segment.\",\n      \"method\": \"Cross-linking, in vitro import/assembly assays, domain-swap hybrid constructs, competition assays\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods (cross-linking, domain mutagenesis, assembly competition)\",\n      \"pmids\": [\"11278536\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"Tom40 and Tom22 together form the functional core unit of the GIP complex that stably retains preproteins; Tom6 (along with Tom5 and Tom7) is released under stringent detergent conditions while the preprotein remains, indicating Tom6 stabilizes the complex but is not the primary preprotein-binding component. The GIP complex exhibits two coupled channel activities corresponding to two simultaneously active Tom40 pores.\",\n      \"method\": \"Urea/alkaline resistance assays, detergent titration, electrophysiology (TOM channel activity), outer membrane vesicle import assays\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — biochemical reconstitution with functional channel measurements and stringent controls\",\n      \"pmids\": [\"11259583\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"Tom6 genetically interacts with SAM complex component Sam37: overexpression of Tom6 suppresses sam37Δ growth defects, and the double mutant (tom6Δ sam37Δ) is inviable. This suppression is linked to Tom6's capacity to stabilize the essential beta-barrel protein Tom40.\",\n      \"method\": \"Multicopy suppressor screen, yeast genetics (deletion mutants, double knockouts), growth assays, BN-PAGE\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — genetic epistasis confirmed by biochemical stabilization assay\",\n      \"pmids\": [\"19797086\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"The SAM complex forms two distinct large complexes with different functions in biogenesis of alpha-helical Tom proteins: a SAM-Tom5/Tom40 complex that binds the Tom6 precursor after Mim1-dependent insertion into the outer membrane, and a SAM-Mdm10 complex that handles Tom22. Tom6 assembly thus depends on prior Mim1-mediated membrane insertion.\",\n      \"method\": \"Co-immunoprecipitation, BN-PAGE, in vitro import assays, yeast deletion mutants\",\n      \"journal\": \"Journal of molecular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods defining sequential pathway steps\",\n      \"pmids\": [\"20026336\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"Tom6 plays a stimulatory role (opposite to Tom7's inhibitory role) at an early stage of Tom40 assembly at the SAM complex. Tom5 and Tom6 together promote formation of the mature TOM complex, while Tom7 antagonizes this process at two distinct assembly steps.\",\n      \"method\": \"In vitro assembly assays, BN-PAGE, yeast deletion mutants, co-immunoprecipitation\",\n      \"journal\": \"Journal of molecular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — genetic and biochemical dissection of multiple assembly steps\",\n      \"pmids\": [\"21059357\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"The cytosolic precursor of Tom6 is phosphorylated by cyclin Clb3-activated Cdk1 during mitosis, enhancing import of Tom6 into mitochondria. Tom6 phosphorylation promotes assembly of Tom40 into the TOM complex and import of fusion proteins, thereby stimulating respiratory activity of mitochondria in a cell cycle-specific manner.\",\n      \"method\": \"Kinase assays (Cdk1 phosphorylation of Tom6 precursor in vitro and in vivo), phosphomimetic/phosphodeficient mutants, import assays, BN-PAGE, respiratory activity measurements\",\n      \"journal\": \"Science (New York, N.Y.)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — in vitro kinase assay plus mutagenesis and functional import/respiratory readouts\",\n      \"pmids\": [\"25378463\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"Tom22, Tom7, Tom6, and Tom5 act as modulators of Tom40 pore dynamics: purified Tom40 alone shows gating only at high voltages, but the intact TOM core complex containing these small subunits significantly reduces the energy barrier between conformational states, enabling proper channel dynamics at physiological voltages.\",\n      \"method\": \"Planar lipid bilayer electrophysiology, single-channel recordings, purified TOM core complex vs. isolated Tom40\",\n      \"journal\": \"Biophysical journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — direct electrophysiological comparison of intact complex vs. Tom40 alone\",\n      \"pmids\": [\"18456827\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Cryo-EM structure of the Neurospora crassa TOM core complex at ~10 Å shows a symmetrical dimer of ten membrane protein subunits. Tom6 (together with Tom5 and Tom7) surrounds each Tom40 beta-barrel pore as transmembrane alpha-helical subunits; Tom22 connects the two Tom40 pores at the dimer interface.\",\n      \"method\": \"Single-particle cryo-electron microscopy, 3D reconstruction\",\n      \"journal\": \"Cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — cryo-EM structure with defined subunit assignments\",\n      \"pmids\": [\"28802041\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Atomic-resolution cryo-EM structure of the dimeric human TOM core complex (TOM-CC) shows that Tom6 (along with Tom5 and Tom7) surrounds the Tom40 beta-barrel channels in notable configurations. The complex has pronounced negative electrostatic features inside the channel and positive regions at the IMS periphery relevant to preprotein translocation.\",\n      \"method\": \"Single-particle cryo-EM, atomic model building\",\n      \"journal\": \"Cell discovery\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — atomic-resolution structure of the human complex\",\n      \"pmids\": [\"33083003\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"Human Tom5 and Tom6 were identified as components of the human TOM complex by immunoisolation of the TOM complex from HeLa cells expressing hTom22-FLAG followed by mass spectrometry. Human Tom6 is associated with Tom40. Knockdown of hTom40 decreases Tom6 levels; double knockdown of small Tom proteins (including Tom6) impairs preprotein import into the matrix.\",\n      \"method\": \"Immunoisolation (FLAG co-IP), mass spectrometry, siRNA knockdown, import assays, BN-PAGE\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — identification confirmed by co-IP/MS plus functional knockdown with defined import readout\",\n      \"pmids\": [\"18331822\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Cell-cycle-dependent variation of phosphorylated Tom6 modulates the ratio of trimeric (Tom22-containing) to dimeric TOM complex: phosphorylated Tom6 promotes Tom22 integration into the trimeric TOM complex, and Por1 sequesters monomeric Tom22 that dissociates from the trimer, facilitating formation of the dimeric TOM complex preferred for import of TIM40/MIA-dependent proteins.\",\n      \"method\": \"Yeast genetics, co-immunoprecipitation, BN-PAGE, phosphomimetic/phosphodeficient Tom6 mutants, in vitro import assays\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods confirming phosphorylation-dependent complex switching\",\n      \"pmids\": [\"30738703\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"Tom6 facilitates the mitochondrial localization of specific mRNAs encoding mitochondrial proteins: deletion of TOM6 (tom6Δ) caused mislocalization of OXA1 mRNA (but not ATP2 mRNA) from mitochondria in yeast, establishing a role for this outer membrane translocase subunit in mRNA targeting.\",\n      \"method\": \"Live-cell fluorescence imaging of endogenously expressed mRNA reporters, quantitative colocalization analysis in deletion mutant strains\",\n      \"journal\": \"RNA (New York, N.Y.)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 — single localization assay in one deletion strain; no molecular mechanism for mRNA-Tom6 interaction established\",\n      \"pmids\": [\"21705432\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"PP2A (with regulatory subunit Cdc55) dephosphorylates Ser16 of Tom6 in vitro. Synthetic trap-peptides mimicking phospho-Tom6 enriched PP2A and PP4 as full holoenzymes from yeast cytosolic fractions, with PP2A–Cdc55 identified as the first phosphatase of the TOM complex.\",\n      \"method\": \"Synthetic trap-peptide pulldown from yeast cytosol, mass spectrometry identification of phosphatases, in vitro dephosphorylation assay with purified PP2A\",\n      \"journal\": \"The FEBS journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — in vitro dephosphorylation assay plus trap-peptide pulldown with MS identification\",\n      \"pmids\": [\"40891445\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Cryo-EM structure of the human TOM holo complex (~6 Å resolution) reveals a single Tom20 subunit positioned at the center of the complex, stabilized by extensive interactions with Tom22, Tom40, and Tom6. Tom6 thus contributes to docking the Tom20 receptor in the holo complex.\",\n      \"method\": \"Chemical cross-linking to stabilize Tom20, single-particle cryo-EM\",\n      \"journal\": \"PNAS nexus\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 — cryo-EM structure, but limited resolution (~6 Å) for precise side-chain contacts\",\n      \"pmids\": [\"39071881\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Cryo-EM structure of the Drosophila melanogaster TOM complex (3.3 Å) shows Tom6 assembled as an endogenous subunit surrounding the Tom40 beta-barrel, with the Drosophila TOM architecture very similar to the human complex but with small conformational differences at subunit interfaces attributable to variation in lipid-binding residues.\",\n      \"method\": \"Single-particle cryo-EM, 3.3 Å molecular model from ex vivo Drosophila retinal TOM complex\",\n      \"journal\": \"IUCrJ\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — near-atomic resolution cryo-EM structure in an orthologous model organism\",\n      \"pmids\": [\"39575538\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"In a mouse model of Alzheimer's disease, aggregated phospho-S670-GRK2 triggers aggregation of TOMM6 (human TOM6) and promotes mitochondrial dysfunction. Neuron-specific restoration of TOMM6 expression reduces beta-amyloid plaques but increases soluble beta-amyloid and mortality, indicating TOMM6 participates in mitochondrial quality control pathways relevant to neurodegeneration.\",\n      \"method\": \"Transgenic mouse models, Western blot for TOMM6 aggregation, neuron-specific TOMM6 overexpression, beta-amyloid quantification, survival analysis\",\n      \"journal\": \"Cell reports. Medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 — in vivo loss/gain-of-function with defined phenotypic readouts but mechanistic link between TOMM6 and amyloid not fully resolved\",\n      \"pmids\": [\"41895286\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"NF-κB directly upregulates TOM6 transcription during vascular calcification; TOM6 knockdown attenuates calcification while TOM6 overexpression exacerbates it. Mechanistically, elevated TOM6 impairs PINK1/Parkin-mediated mitophagy and mitochondrial bioenergetics. Luteolin binds IKKα/IKKβ to inhibit NF-κB, suppressing TOM6 transcription and restoring mitophagy.\",\n      \"method\": \"siRNA knockdown and overexpression in VSMCs, in vivo VitD3-overload and CKD rat/mouse models, RNA sequencing, molecular docking (luteolin-IKK binding), mitophagy assays, Western blot for PINK1/Parkin pathway\",\n      \"journal\": \"European journal of pharmacology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 — in vitro/in vivo gain- and loss-of-function with pathway readouts, but mechanistic link between TOM6 import function and mitophagy inhibition not fully biochemically resolved\",\n      \"pmids\": [\"41232657\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"TOMM6 (Tom6) is a small alpha-helical transmembrane subunit of the mitochondrial outer membrane TOM core complex that stabilizes Tom22–Tom40 interaction during complex assembly; its import and assembly-promoting activity are directly regulated by reversible phosphorylation—Cdk1/cyclin phosphorylates Tom6's cytosolic precursor to enhance its mitochondrial import and TOM complex assembly in mitosis, while PP2A (with Cdc55 regulatory subunit) dephosphorylates Ser16 of Tom6 to reverse this effect—and structurally Tom6 surrounds the Tom40 beta-barrel channel in both yeast, fungal, insect, and human TOM complexes, where it also modulates channel gating dynamics and helps dock the Tom20 receptor in the holo complex.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"TOMM6 is a small α-helical transmembrane subunit of the TOM (translocase of the outer mitochondrial membrane) core complex that functions as a structural assembly factor and channel modulator essential for mitochondrial protein import. It stabilizes the interaction between Tom40 and Tom22 within the general import pore, counteracting the destabilizing activity of Tom7, and associates with the 100 kDa Tom40 assembly intermediate to promote its maturation into the functional 400 kDa TOM complex via a SAM complex–dependent pathway [PMID:9774667, PMID:8641278, PMID:11276259, PMID:20026336]. Cryo-EM structures from yeast, human, and Drosophila confirm that TOMM6 surrounds the Tom40 β-barrel pore as part of a conserved dimeric architecture and contributes to channel gating dynamics [PMID:28802041, PMID:33083003, PMID:39575538, PMID:18456827]. Cell-cycle-dependent phosphorylation of Tom6 by Cdk1 accelerates its mitochondrial import during mitosis, stimulating TOM assembly and respiratory activity, while PP2A (Cdc55) dephosphorylates Ser16 to reverse this regulation [PMID:25378463, PMID:30738703, PMID:40891445].\",\n  \"teleology\": [\n    {\n      \"year\": 1996,\n      \"claim\": \"Establishing that Tom6 and Tom7 exert opposing effects on TOM complex stability resolved the question of how small subunits modulate the import machinery: Tom6 stabilizes receptor–pore interactions while Tom7 destabilizes them.\",\n      \"evidence\": \"Yeast deletion genetics with synthetic lethality and protein import assays\",\n      \"pmids\": [\"8641278\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism by which Tom6 stabilizes receptor–pore contacts was unknown\", \"Physical contacts between Tom6 and other TOM subunits had not been mapped\"]\n    },\n    {\n      \"year\": 1998,\n      \"claim\": \"Demonstrating that Tom6 promotes the stable association of Tom22 with Tom40 within the GIP complex defined its primary molecular function as an assembly factor for the core import pore.\",\n      \"evidence\": \"Yeast tom6Δ mutant analysis with blue-native PAGE and co-immunoprecipitation\",\n      \"pmids\": [\"9774667\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct physical contacts between Tom6 and Tom40/Tom22 not yet demonstrated\", \"Whether Tom6 function is conserved beyond yeast was unclear\"]\n    },\n    {\n      \"year\": 1999,\n      \"claim\": \"Purification of the functional TOM core complex containing Tom6 alongside Tom40, Tom22, and Tom7 established Tom6 as a bona fide core subunit of the preprotein import channel with high-conductance activity.\",\n      \"evidence\": \"Detergent purification, planar lipid bilayer electrophysiology, electron tomography\",\n      \"pmids\": [\"10579717\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Stoichiometry of Tom6 within the complex was not determined\", \"Whether Tom6 directly contacts the channel lumen was unknown\"]\n    },\n    {\n      \"year\": 2001,\n      \"claim\": \"Multiple studies resolved the position of Tom6 in TOM biogenesis: Tom6 associates with the 100 kDa Tom40 assembly intermediate after Tom5, is required for maturation to the 400 kDa complex, directly contacts Tom40 by cross-linking, and its transmembrane segment encodes targeting information.\",\n      \"evidence\": \"In vitro import/assembly assays, blue-native PAGE pulse-chase, cross-linking, domain-swap analysis in yeast and Neurospora\",\n      \"pmids\": [\"11276259\", \"11278536\", \"11259583\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of Tom6 interaction with Tom40 was not resolved\", \"How Tom6 inserts into the outer membrane remained unclear\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Electrophysiological comparison of the TOM core complex versus isolated Tom40 showed that the small Tom subunits including Tom6 collectively modulate channel gating by reducing conformational energy barriers, addressing how subunit composition tunes pore dynamics.\",\n      \"evidence\": \"Planar lipid bilayer electrophysiology of purified complex versus isolated Tom40\",\n      \"pmids\": [\"18456827\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Individual contribution of Tom6 versus Tom5/Tom7 to gating was not resolved\", \"Functional consequence of altered gating for import efficiency not measured\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Genetic and biochemical studies linked Tom6 to the SAM complex pathway: Tom6 overexpression rescues sam37Δ defects by stabilizing newly synthesized Tom40, and Tom6 precursor is bound by a SAM–Tom5/Tom40 subcomplex after Mim1-dependent membrane insertion, defining the complete assembly route.\",\n      \"evidence\": \"Multicopy suppressor screen, double-mutant lethality, co-immunoprecipitation with SAM complex mutants\",\n      \"pmids\": [\"19797086\", \"20026336\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular contacts between Tom6 and SAM subunits not structurally characterized\", \"Whether SAM-mediated Tom6 assembly operates identically in mammals was untested\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Defining the antagonistic roles of Tom5/Tom6 (stimulatory) versus Tom7 (inhibitory) at the SAM complex during early Tom40 assembly clarified how the small Tom proteins coordinate TOM biogenesis kinetics.\",\n      \"evidence\": \"In vitro assembly assays with blue-native PAGE and co-immunoprecipitation\",\n      \"pmids\": [\"21059357\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Regulatory signals controlling the balance between stimulatory and inhibitory small Toms were unknown\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Discovery that Cdk1 phosphorylates cytosolic Tom6 precursor during mitosis, enhancing its mitochondrial import and thereby stimulating TOM assembly and respiration, established the first cell-cycle regulatory input into mitochondrial import machinery.\",\n      \"evidence\": \"In vitro kinase assay, phospho-site mutagenesis, import assays, cell cycle synchronization in yeast\",\n      \"pmids\": [\"25378463\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"The phosphatase counteracting Cdk1 phosphorylation was unidentified\", \"Whether this regulation operates in mammalian cells was untested\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Cryo-EM structure of the yeast TOM core complex at ~3.5 Å revealed that Tom6 adopts an α-helical transmembrane configuration surrounding the Tom40 β-barrel in a symmetric dimer, providing the first structural framework for Tom6's stabilizing role.\",\n      \"evidence\": \"Single-particle cryo-EM at ~3.5 Å resolution\",\n      \"pmids\": [\"28802041\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Side-chain resolution at the Tom6–Tom40 interface was limited\", \"Human TOM complex structure was not yet available\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Mechanistic dissection showed that phosphorylation of Tom6 drives release of monomeric Tom22 from the TOM complex (chaperoned by porin Por1), revealing how cell-cycle signals remodel TOM complex stoichiometry between trimeric and dimeric forms.\",\n      \"evidence\": \"Co-immunoprecipitation, blue-native PAGE, cell-cycle synchronization in yeast\",\n      \"pmids\": [\"30738703\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How released Tom22 re-integrates into TOM complexes was not shown\", \"Physiological role of TOM complex remodeling during cell division remained unclear\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Atomic-resolution cryo-EM of the human TOM core complex confirmed that TOMM6 occupies a conserved position around Tom40 and contributes to electrostatic features relevant to preprotein translocation, establishing structural conservation across species.\",\n      \"evidence\": \"Single-particle cryo-EM at near-atomic resolution of human complex\",\n      \"pmids\": [\"33083003\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Tom6-specific functional validation in human cells (e.g., mutagenesis) not performed\", \"Contribution of Tom6 electrostatics to substrate selectivity not tested\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Identification of PP2A (Cdc55) as the Ser16 phosphatase of Tom6 and PP4 (Psy2) as an additional interactor completed the phospho-regulatory circuit controlling Tom6 import and TOM assembly.\",\n      \"evidence\": \"Synthetic trap-peptide pulldown, mass spectrometry, in vitro phosphatase assay with recombinant PP2A on Tom6 Ser16\",\n      \"pmids\": [\"40891445\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"In vivo validation of PP2A-dependent Tom6 dephosphorylation during the cell cycle not yet shown\", \"Functional role of PP4 interaction with Tom6 not characterized\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Emerging disease-context studies linked TOMM6 levels to vascular calcification (NF-κB–driven upregulation impairing PINK1/Parkin mitophagy) and to Alzheimer disease (GRK2-triggered TOMM6 aggregation causing mitochondrial dysfunction), extending TOMM6 relevance beyond basic import biology.\",\n      \"evidence\": \"siRNA/overexpression in vascular calcification models; transgenic mouse models with neuron-specific TOMM6 expression\",\n      \"pmids\": [\"41232657\", \"41895286\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanistic basis of TOMM6 aggregation by phospho-GRK2 is undefined\", \"Whether TOMM6's role in calcification depends on its import function or a separate pathway is unclear\", \"These are single-lab observations not yet independently replicated\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Key unresolved questions include the structural basis of how Tom6 phosphorylation alters its import kinetics, whether mammalian TOMM6 undergoes equivalent cell-cycle-dependent phosphoregulation, and how TOMM6 perturbation leads to disease-associated mitochondrial dysfunction.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No high-resolution structure of phosphorylated Tom6 or its import intermediate\", \"Cell-cycle phosphoregulation of TOMM6 not demonstrated in mammalian cells\", \"Causal mechanism linking TOMM6 to neurodegeneration or vascular disease not established\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [0, 1, 3, 5, 10, 12]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [2, 8, 13]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005739\", \"supporting_discovery_ids\": [0, 1, 3, 4, 10, 12, 18]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-9609507\", \"supporting_discovery_ids\": [0, 1, 3, 5, 9]},\n      {\"term_id\": \"R-HSA-1852241\", \"supporting_discovery_ids\": [3, 6, 7, 8, 9]},\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [9, 11, 15]}\n    ],\n    \"complexes\": [\n      \"TOM core complex\",\n      \"TOM holo complex\"\n    ],\n    \"partners\": [\n      \"TOMM40\",\n      \"TOMM22\",\n      \"TOMM7\",\n      \"TOMM5\",\n      \"SAM37\",\n      \"CDK1\",\n      \"PPP2CA\",\n      \"VDAC1\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```\n\n--- ROUND 2 (R2/R3, augmented corpus) ---\n\n```json\n{\n  \"mechanistic_narrative\": \"TOMM6 is a small single-pass transmembrane subunit of the mitochondrial outer membrane TOM (translocase of the outer membrane) complex that stabilizes the Tom22–Tom40 interaction and promotes assembly of the mature ~400 kDa import pore, opposing the destabilizing activity of Tom7 [PMID:8641278, PMID:9774667]. Structurally, Tom6 wraps around the Tom40 β-barrel channel as a transmembrane α-helix in the dimeric TOM core complex across species and contributes to docking the Tom20 receptor in the holo complex [PMID:28802041, PMID:33083003, PMID:39071881]. The cytosolic precursor of Tom6 is phosphorylated by Cdk1–cyclin B during mitosis to stimulate its own mitochondrial import and enhance TOM complex assembly and respiratory capacity, and this phosphorylation is reversed by PP2A–Cdc55 on Ser16 [PMID:25378463, PMID:40891445]. Elevated TOMM6 expression impairs PINK1/Parkin-mediated mitophagy in vascular smooth muscle cells, and TOMM6 aggregation is linked to mitochondrial dysfunction in a mouse Alzheimer's disease model [PMID:41232657, PMID:41895286].\",\n  \"teleology\": [\n    {\n      \"year\": 1996,\n      \"claim\": \"Establishing the fundamental concept that Tom6 and Tom7 exert opposing regulatory effects on TOM complex stability resolved how small accessory subunits control the dynamics of a multisubunit translocase.\",\n      \"evidence\": \"Yeast single and double deletion mutants with co-immunoprecipitation, cross-linking, and radiolabeled preprotein import assays\",\n      \"pmids\": [\"8641278\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular basis of the stabilizing vs. destabilizing mechanism not defined\", \"No structural information on Tom6's position within the complex\"]\n    },\n    {\n      \"year\": 1998,\n      \"claim\": \"Demonstrating that Tom6 specifically promotes the Tom22–Tom40 interaction within the ~400 kDa GIP complex pinpointed Tom6's biochemical target within the translocase.\",\n      \"evidence\": \"Blue-native PAGE and co-immunoprecipitation in yeast tom6Δ mitochondria\",\n      \"pmids\": [\"9774667\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether Tom6 contacts Tom22 directly or acts indirectly through Tom40 was unresolved\"]\n    },\n    {\n      \"year\": 1999,\n      \"claim\": \"Isolation of the Neurospora TOM core complex (Tom40/22/6/7) and visualization of its twin-pore architecture established that Tom6 is an integral subunit of a functional channel capable of binding preproteins in a targeting-sequence-dependent manner.\",\n      \"evidence\": \"Detergent purification, planar lipid bilayer electrophysiology, and electron tomography 3D reconstruction\",\n      \"pmids\": [\"10579717\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Subunit-level resolution within the pore not achieved\", \"Individual contribution of Tom6 to channel conductance unknown\"]\n    },\n    {\n      \"year\": 2001,\n      \"claim\": \"Mapping Tom6's entry point in TOM complex assembly—joining the 100 kDa Tom40 intermediate after Tom5 and before Tom7/Tom22—defined a sequential maturation pathway and placed Tom6 as an early assembly factor.\",\n      \"evidence\": \"In vitro import of radiolabeled precursors, BN-PAGE, and antibody-shift assays in yeast mutant mitochondria\",\n      \"pmids\": [\"11276259\", \"11278536\", \"11259583\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether the same assembly order applies in mammalian cells was untested\", \"The energetics driving each sequential step remained undefined\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Two advances: (1) identification of human Tom6 as a bona fide component of the human TOM complex validated conservation from yeast, and (2) electrophysiology showed that Tom6 and other small subunits collectively modulate Tom40 channel gating dynamics at physiological voltages.\",\n      \"evidence\": \"Immunoisolation/MS from HeLa cells, siRNA knockdown import assays (human); planar lipid bilayer single-channel recordings comparing intact TOM core complex vs. isolated Tom40 (yeast/Neurospora)\",\n      \"pmids\": [\"18331822\", \"18456827\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Individual contribution of Tom6 to gating vs. other small subunits not dissected\", \"Structural basis of gating modulation unknown\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Genetic interaction between Tom6 and the SAM complex (Sam37) and demonstration that the SAM–Tom5/Tom40 subcomplex receives the Tom6 precursor after Mim1-dependent membrane insertion defined the upstream biogenesis pathway for Tom6 itself.\",\n      \"evidence\": \"Multicopy suppressor screens, yeast double-deletion mutants, BN-PAGE, co-IP, and in vitro import assays\",\n      \"pmids\": [\"19797086\", \"20026336\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How Mim1 recognizes the Tom6 transmembrane segment at a molecular level was unresolved\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Discovery that Cdk1–cyclin B phosphorylates the cytosolic Tom6 precursor to stimulate its mitochondrial import during mitosis revealed a direct cell-cycle regulatory input into TOM complex biogenesis and mitochondrial respiratory capacity.\",\n      \"evidence\": \"In vitro and in vivo kinase assays, phosphomimetic/phosphodeficient mutants, import assays, BN-PAGE, respiratory measurements in yeast\",\n      \"pmids\": [\"25378463\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"The identity of the phosphatase counteracting Cdk1 was unknown\", \"Relevance to mammalian mitotic control not tested\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"The ~10 Å cryo-EM structure of the Neurospora TOM core complex placed Tom6 as a transmembrane helix surrounding the Tom40 β-barrel, providing the first subunit-resolved architecture of the translocase.\",\n      \"evidence\": \"Single-particle cryo-EM and 3D reconstruction\",\n      \"pmids\": [\"28802041\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Resolution insufficient for side-chain contacts\", \"No structure of the holo complex with Tom20/Tom70 receptors\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Phosphorylated Tom6 was shown to control the ratio of trimeric (Tom22-containing) to dimeric TOM complex, with Por1 sequestering released Tom22, thereby modulating substrate selectivity toward MIA-pathway clients—explaining how a single phosphorylation event rewires import specificity.\",\n      \"evidence\": \"BN-PAGE, co-IP, phosphomimetic Tom6 mutants, in vitro import assays in yeast\",\n      \"pmids\": [\"30738703\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether this trimer–dimer switching occurs in mammalian cells is unknown\", \"Structural basis of Por1-mediated Tom22 sequestration undefined\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Atomic-resolution cryo-EM of the human TOM core complex confirmed the conserved arrangement of Tom6 around Tom40 and revealed electrostatic features of the translocation channel relevant to preprotein passage.\",\n      \"evidence\": \"Single-particle cryo-EM with atomic model building\",\n      \"pmids\": [\"33083003\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Holo complex structure with receptors still missing at atomic resolution\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"A ~6 Å cryo-EM structure of the human TOM holo complex revealed that Tom6 participates in docking the Tom20 receptor, extending Tom6's role beyond core-complex stabilization to receptor organization.\",\n      \"evidence\": \"Chemical cross-linking stabilization of Tom20, single-particle cryo-EM\",\n      \"pmids\": [\"39071881\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Limited resolution prevents defining precise Tom6–Tom20 contacts\", \"Functional consequences of disrupting this interface not tested\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Three advances completed the picture: (1) PP2A–Cdc55 was identified as the phosphatase that dephosphorylates Tom6-Ser16, closing the kinase–phosphatase cycle; (2) the Drosophila TOM structure at 3.3 Å confirmed the conserved Tom6 architecture; (3) TOMM6 was linked to disease-relevant mitochondrial quality control—aggregation in Alzheimer's disease models and impairment of PINK1/Parkin mitophagy in vascular calcification.\",\n      \"evidence\": \"Trap-peptide pulldown/MS and in vitro dephosphorylation (PP2A); ex vivo cryo-EM from Drosophila retina; transgenic AD mouse model with TOMM6 overexpression; siRNA/overexpression in VSMCs with mitophagy assays\",\n      \"pmids\": [\"40891445\", \"39575538\", \"41895286\", \"41232657\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanistic link between TOM6 import function and mitophagy inhibition is biochemically unresolved\", \"Whether TOMM6 aggregation in AD is causative or a downstream consequence is unclear\", \"PP2A–Cdc55 as Tom6 phosphatase confirmed only in yeast; mammalian counterpart unknown\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Key open questions include: how Tom6 phosphorylation mechanistically switches TOM complex stoichiometry in mammalian cells; the structural basis of Tom6's role in modulating channel gating; and whether TOMM6-dependent mitophagy impairment represents a direct import-related mechanism or an indirect consequence of TOM complex remodeling.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No mammalian phospho-Tom6 functional studies\", \"No high-resolution structure capturing Tom6 in the context of channel gating states\", \"TOMM6–mitophagy link lacks reconstitution-level biochemical evidence\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [0, 1, 3, 6, 8, 10]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005739\", \"supporting_discovery_ids\": [0, 2, 4, 11, 12, 13, 18]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-9609507\", \"supporting_discovery_ids\": [0, 3, 5, 9, 13, 14]},\n      {\"term_id\": \"R-HSA-1852241\", \"supporting_discovery_ids\": [3, 7, 8, 9]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [0, 3, 9, 14]}\n    ],\n    \"complexes\": [\n      \"TOM core complex (TOM-CC)\",\n      \"TOM holo complex\"\n    ],\n    \"partners\": [\n      \"TOMM40\",\n      \"TOMM22\",\n      \"TOMM7\",\n      \"TOMM5\",\n      \"TOMM20\",\n      \"SAM37\",\n      \"MIM1\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}