{"gene":"CHCHD3","run_date":"2026-06-09T22:57:18","timeline":{"discoveries":[{"year":2010,"finding":"ChChd3 (CHCHD3/Mic19) is a peripheral protein of the mitochondrial inner membrane facing the intermembrane space. RNAi knockdown in HeLa cells caused mitochondrial fragmentation, reduced OPA1 protein levels, impaired fusion, and aberrant cristae with reduced crista junction opening diameter (~50% reduction). ChChd3 interacts with inner membrane proteins mitofilin and OPA1, and outer membrane protein Sam50; knockdown led to near-complete loss of mitofilin and Sam50, establishing ChChd3 as a scaffolding protein stabilizing complexes that maintain crista architecture and protein import.","method":"RNAi knockdown in HeLa cells, Co-IP/binding partner analysis, ultrastructural analysis (electron microscopy), oxygen consumption and glycolytic rate measurements","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal binding partner identification, RNAi with defined structural and functional phenotypes, multiple orthogonal methods (EM ultrastructure, biochemistry, metabolic flux), foundational paper replicated by subsequent work","pmids":["21081504"],"is_preprint":false},{"year":2007,"finding":"CHCHD3 (ChChd3) was identified as a novel substrate of cAMP-dependent protein kinase (PKA) using an analog-sensitive PKA catalytic subunit (M120G mutant) with bulky N6-substituted ATP analogs, establishing PKA as a writer of CHCHD3 phosphorylation.","method":"Chemical genetics approach with analog-sensitive PKA catalytic subunit, in vitro kinase assay with N6-substituted ATP analogs, mass spectrometry substrate identification","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — in vitro kinase assay with engineered substrate trapping, single lab, single paper","pmids":["17242405"],"is_preprint":false},{"year":2012,"finding":"CHCHD3 import into the mitochondrial IMS requires both N-terminal myristoylation and the C-terminal CHCH domain. Myristoylation promotes binding to the outer membrane; the CHCH domain mediates translocation across the outer membrane. The disulfide relay via Mia40 occurs preferentially between Cys193 (second cysteine in helix 1) and Mia40 Cys55. Each of the four CHCH domain cysteines is essential for protein folding and binding to mitofilin and Sam50, but not for import per se.","method":"Cysteine mutagenesis, myristoylation site mutagenesis (G2A), in vitro import assays, binding assays to Mia40/mitofilin/Sam50, subcellular fractionation","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Moderate — systematic mutagenesis combined with import assays and binding partner analysis, multiple orthogonal methods in single rigorous study","pmids":["23019327"],"is_preprint":false},{"year":2015,"finding":"MIC19 (CHCHD3) undergoes oxidation in mitochondria and requires the MIA pathway for mitochondrial localization. Yeast Mic19 exists in two redox forms; the intramolecular disulfide-bonded form is specifically bound to Mic60 of the MICOS complex. Mic19 oxidation is not essential for MICOS integration but promotes MICOS assembly and proper inner membrane morphology.","method":"Redox state analysis (non-reducing SDS-PAGE), MIA pathway mutant analysis, Co-IP (Mic19-Mic60 interaction), yeast genetics, immunofluorescence","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP, redox biochemistry with multiple genetic and biochemical orthogonal methods, replicated in both human and yeast","pmids":["26416881"],"is_preprint":false},{"year":2017,"finding":"Using genetically encoded tags (miniSOG and APEX2) and electron tomography, Mic19 (CHCHD3) was localized at nanoscale resolution to crista junctions, distributed in a network along the mitochondrial periphery, and enriched inside cristae in cardiac and astrocyte cell lines. Mic19 was found associated with cytochrome c oxidase subunit IV at crista junctions.","method":"Genetic tagging with miniSOG and APEX2, electron tomography, subcellular fractionation","journal":"Journal of cell science","confidence":"High","confidence_rationale":"Tier 1 / Moderate — direct nanoscale structural localization with APEX2/miniSOG and electron tomography, two orthogonal EM tags, two cell lines","pmids":["28808085"],"is_preprint":false},{"year":2018,"finding":"MIC19 (CHCHD3) is N-myristoylated at its N-terminus. In vitro and in vivo metabolic labeling confirmed N-myristoylation. G2A (non-myristoylated) mutant analysis showed that myristoylation is required for proper mitochondrial targeting and membrane binding of MIC19. Additionally, myristoylation of MIC19 is required for the protein-protein interaction between MIC19 and SAMM50.","method":"In vitro and in vivo metabolic labeling with myristate, G2A mutagenesis, immunofluorescence, subcellular fractionation, co-immunoprecipitation","journal":"PloS one","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro and in vivo labeling with mutagenesis and Co-IP, multiple orthogonal methods confirming myristoylation and its functional requirement","pmids":["30427857"],"is_preprint":false},{"year":2019,"finding":"Mic19 (CHCHD3) directly interacts with outer membrane protein Sam50 and inner membrane protein Mic60 to form the Sam50-Mic19-Mic60 axis, which connects SAM and MICOS complexes to assemble the MIB supercomplex and mediates mitochondrial outer-inner membrane contact. OMA1 protease cleaves Mic19 at its N-terminus under physiological stress, disrupting this axis and causing loss of crista junctions, abnormal cristae distribution, and reduced ATP production. Sam50 acts as an anchoring point at the outer membrane guiding crista junction formation.","method":"Co-IP, OMA1-mediated cleavage assays, MIB supercomplex analysis, ATP production measurements, mitochondrial morphology analysis, electron microscopy of cristae","journal":"Cell death and differentiation","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP, protease cleavage assay, multiple functional readouts (ATP, EM ultrastructure, crista junction morphology), replicated across conditions","pmids":["31097788"],"is_preprint":false},{"year":2023,"finding":"Fasting induces MIC19 (CHCHD3) upregulation in mouse liver, promoting cristae formation. Enforced hepatic MIC19 expression promotes mitochondrial respiration, fatty acid oxidation, and suppresses gluconeogenesis. MIC19-driven cristae formation increases uridine phosphorylase UPP2 activity and uracil accumulation, which signals to promote locomotion.","method":"Comparative mouse proteomics, hepatic MIC19 transgenic overexpression, Seahorse respirometry, metabolite profiling, dietary uracil supplementation experiments","journal":"Cell metabolism","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vivo transgenic model with multiple metabolic readouts and metabolite profiling, single lab study","pmids":["37473754"],"is_preprint":false},{"year":2024,"finding":"Mic19 (CHCHD3) regulates ER-mitochondria contacts through the EMC2-SLC25A46-Mic19 axis. Liver-specific Mic19 knockout in mice leads to reduction of ER-mitochondrial contacts, mitochondrial lipid metabolism disorder, disorganization of mitochondrial cristae, and mitochondrial unfolded protein stress response in hepatocytes, impairing fatty acid β-oxidation and spontaneously triggering NASH and liver fibrosis. Re-expression of Mic19 in LKO hepatocytes rescued liver disease.","method":"Liver-specific conditional knockout (LKO), ER-mitochondria contact site quantification, mitochondrial fractionation, fatty acid oxidation assays, hepatic rescue re-expression experiments, in vivo mouse models","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 / Strong — conditional KO with rescue experiment, multiple orthogonal functional readouts (ER-mito contacts, lipid metabolism, histology), in vivo model","pmids":["38168065"],"is_preprint":false},{"year":2024,"finding":"ASB1 E3 ubiquitin ligase interacts with CHCHD3 and promotes its degradation via K48-linked ubiquitination. Loss of ASB1 stabilizes CHCHD3, which activates ROS signaling to promote prostate cancer cell proliferation, clonogenicity, and migration.","method":"Quantitative mass spectrometry interactome analysis, co-immunoprecipitation, cycloheximide chase assay, ubiquitination assay, cell rescue experiments","journal":"American journal of cancer research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP, ubiquitination assay with K48 linkage specificity, cycloheximide chase, and rescue experiments, single lab","pmids":["39113857"],"is_preprint":false},{"year":2025,"finding":"Under hypoxic conditions, HIF-1α binds the USP3 promoter to upregulate USP3 expression, which in turn stabilizes MIC19 (CHCHD3) through K48-linked deubiquitination, preventing its proteasomal degradation and promoting NSCLC progression.","method":"ChIP assay (HIF-1α at USP3 promoter), ubiquitination assay, co-immunoprecipitation (USP3-MIC19), in vitro cell proliferation/invasion assays, in vivo xenograft mouse model","journal":"Acta pharmacologica Sinica","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ChIP, Co-IP, ubiquitination assay with deubiquitination specificity, in vivo validation, single lab","pmids":["40770539"],"is_preprint":false},{"year":2026,"finding":"SLC25A6 directly interacts with MIC60 and competitively inhibits MIC19 (CHCHD3) binding to MIC60, disrupting the MICOS complex. A SLC25A6 T126A mutant failed to bind MIC60, abrogating its ability to destabilize MICOS and cause mitofission. This mechanistically links metabolic stress to mitochondrial fragmentation via displacement of MIC19 from MIC60.","method":"Co-immunoprecipitation (SLC25A6-MIC60, competitive with MIC19), site-directed mutagenesis (T126A), mitochondrial morphology analysis, apoptosis assays","journal":"Cell death & disease","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP with competitive binding assay and mutagenesis validation, single lab study","pmids":["42020360"],"is_preprint":false},{"year":2026,"finding":"CHCHD3 knockdown in lung adenocarcinoma cells impaired mitochondrial energy metabolism and caused excessive ROS production. IP-MS and Co-IP validated SAMM50 and VDAC1/2 as direct CHCHD3 binding partners, with disruption of these interactions linked to ROS accumulation.","method":"IP-MS, co-immunoprecipitation, Seahorse metabolic analysis, ROS measurement, cell cycle analysis, apoptosis assays","journal":"Anti-cancer agents in medicinal chemistry","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single Co-IP/IP-MS validation of binding partners, single lab, limited mechanistic follow-up on VDAC1/2 interaction","pmids":["42261148"],"is_preprint":false}],"current_model":"CHCHD3 (Mic19) is a peripheral mitochondrial inner membrane protein in the IMS that is imported via N-terminal myristoylation and a Mia40-dependent disulfide relay through its CHCH domain; once imported, its oxidized (disulfide-bonded) form associates with Mic60 to nucleate the MICOS complex at crista junctions, where it forms a Sam50-Mic19-Mic60 axis bridging outer and inner membranes to organize cristae architecture, maintain ATP production, and regulate ER-mitochondria contacts for lipid metabolism. Its stability is controlled post-translationally by OMA1-mediated cleavage (disrupting the axis under stress), K48-linked ubiquitination by ASB1 (promoting degradation), and K48-linked deubiquitination by USP3 (stabilizing it under hypoxia downstream of HIF-1α), while PKA-mediated phosphorylation was the original modification identified for this protein."},"narrative":{"mechanistic_narrative":"CHCHD3 (Mic19) is a peripheral protein of the mitochondrial inner membrane facing the intermembrane space that functions as a scaffolding subunit organizing crista junction architecture and supporting oxidative metabolism [PMID:21081504]. It is imported into the IMS through a two-signal mechanism: N-terminal myristoylation directs binding to the outer membrane, while its C-terminal CHCH domain mediates translocation and is captured by a Mia40-dependent disulfide relay (Cys193–Mia40 Cys55), and the four CHCH cysteines are required for folding and partner binding rather than import itself [PMID:23019327, PMID:30427857]. Once oxidized, the intramolecular disulfide-bonded form selectively engages Mic60 to drive MICOS assembly and proper inner membrane morphology [PMID:26416881]. CHCHD3 directly bridges the outer-membrane Sam50 and inner-membrane Mic60 to form the Sam50-Mic19-Mic60 axis that unites the SAM and MICOS complexes into the MIB supercomplex and maintains crista junctions and ATP production [PMID:31097788]; this axis is dismantled when OMA1 cleaves CHCHD3 at its N-terminus under stress [PMID:31097788] or when SLC25A6 competitively displaces CHCHD3 from Mic60, causing MICOS disruption and mitochondrial fission [PMID:42020360]. Beyond cristae shaping, CHCHD3 organizes ER-mitochondria contact sites via an EMC2-SLC25A46-Mic19 axis to support mitochondrial lipid metabolism and fatty acid β-oxidation, and hepatic loss spontaneously triggers NASH and liver fibrosis that is reversed by re-expression [PMID:38168065]. Its abundance is set post-translationally by ASB1-mediated K48 ubiquitination driving degradation and by USP3-mediated K48 deubiquitination that stabilizes it under hypoxia downstream of HIF-1α, with both axes implicated in cancer cell proliferation through ROS signaling [PMID:39113857, PMID:40770539].","teleology":[{"year":2007,"claim":"Before any mitochondrial role was known, CHCHD3 was identified as a phosphorylation substrate, providing the first molecular handle on the protein.","evidence":"Chemical-genetic analog-sensitive PKA with N6-substituted ATP analogs and MS substrate identification","pmids":["17242405"],"confidence":"Medium","gaps":["Phosphosite(s) on CHCHD3 not mapped to a function","No link established between PKA phosphorylation and MICOS/cristae roles","Single in vitro study"]},{"year":2010,"claim":"Established CHCHD3 as a structural scaffold of the inner membrane whose loss collapses crista architecture and destabilizes import/morphology complexes, defining its core cellular role.","evidence":"RNAi in HeLa cells with Co-IP partner mapping, EM ultrastructure, and metabolic flux measurements","pmids":["21081504"],"confidence":"High","gaps":["Mechanism of how scaffolding stabilizes partners not resolved","Direct vs indirect nature of OPA1 effect unclear","Import-relay details not addressed"]},{"year":2012,"claim":"Resolved how CHCHD3 reaches the IMS, separating the myristoylation-dependent membrane-binding step from CHCH-domain-mediated translocation and the Mia40 disulfide relay.","evidence":"Cysteine and G2A mutagenesis with in vitro import and Mia40/mitofilin/Sam50 binding assays","pmids":["23019327"],"confidence":"High","gaps":["In vivo myristoyltransferase not identified here","Redox state of mature protein in cells not quantified","How cysteine oxidation gates partner binding unresolved"]},{"year":2015,"claim":"Showed that the oxidized, disulfide-bonded form of CHCHD3 is the species that binds Mic60, linking redox state to MICOS assembly competence.","evidence":"Non-reducing SDS-PAGE redox analysis, MIA pathway mutants, and reciprocal Co-IP in yeast and human cells","pmids":["26416881"],"confidence":"High","gaps":["Stimuli that shift CHCHD3 redox state in vivo unknown","Quantitative contribution of oxidation to morphology not isolated","Reductase/regulators not identified"]},{"year":2017,"claim":"Pinpointed CHCHD3 to crista junctions at nanoscale resolution and associated it with respiratory machinery, anchoring its function spatially.","evidence":"miniSOG/APEX2 genetic EM tagging and electron tomography in cardiac and astrocyte lines","pmids":["28808085"],"confidence":"High","gaps":["Functional consequence of cytochrome c oxidase subunit IV association untested","Dynamics of localization not captured","Cell-type generality beyond two lines unaddressed"]},{"year":2019,"claim":"Defined the Sam50-Mic19-Mic60 axis as the physical bridge connecting SAM and MICOS into the MIB supercomplex and showed OMA1 cleavage as a stress-responsive off-switch controlling crista junctions and ATP output.","evidence":"Reciprocal Co-IP, OMA1 cleavage assays, MIB supercomplex analysis, ATP and EM cristae readouts","pmids":["31097788"],"confidence":"High","gaps":["Trigger and regulation of OMA1 cleavage of CHCHD3 not fully defined","Stoichiometry of the axis unresolved","Structural basis of bridging not determined"]},{"year":2023,"claim":"Connected CHCHD3-driven cristae formation to whole-organism physiology, showing fasting-induced upregulation reprograms hepatic respiration and a uracil-UPP2 signaling output.","evidence":"Mouse liver proteomics, hepatic transgenic overexpression, respirometry, and metabolite profiling","pmids":["37473754"],"confidence":"Medium","gaps":["Mechanism coupling cristae density to UPP2 activity unresolved","Generality beyond liver unknown","Single-lab in vivo model"]},{"year":2024,"claim":"Extended CHCHD3 function beyond cristae to ER-mitochondria contact organization via an EMC2-SLC25A46-Mic19 axis required for lipid metabolism, with hepatic loss causing reversible NASH.","evidence":"Liver-specific conditional knockout with rescue, contact-site quantification, fatty acid oxidation assays","pmids":["38168065"],"confidence":"High","gaps":["Molecular detail of how the axis tethers ER and mitochondria not resolved","Relationship between MICOS and contact-site roles unclear","Direct EMC2/SLC25A46 binding interfaces undefined"]},{"year":2024,"claim":"Identified ASB1 as an E3 ligase that destabilizes CHCHD3 via K48 ubiquitination, placing CHCHD3 abundance under proteostatic control with consequences for ROS and tumor cell behavior.","evidence":"Interactome MS, Co-IP, cycloheximide chase, ubiquitination and rescue assays in prostate cancer cells","pmids":["39113857"],"confidence":"Medium","gaps":["Ubiquitinated residues on CHCHD3 not mapped","How stabilized CHCHD3 activates ROS signaling unresolved","Single-lab study"]},{"year":2025,"claim":"Showed the opposing arm of CHCHD3 proteostasis: hypoxic HIF-1α induces USP3, which deubiquitinates and stabilizes CHCHD3 to promote tumor progression.","evidence":"ChIP for HIF-1α at the USP3 promoter, USP3-MIC19 Co-IP, ubiquitination assays, and xenograft model","pmids":["40770539"],"confidence":"Medium","gaps":["Deubiquitination site specificity not mapped","Whether USP3 and ASB1 act on the same lysines unknown","Single-lab study"]},{"year":2026,"claim":"Demonstrated a competitive regulatory mechanism in which SLC25A6 binds Mic60 and displaces CHCHD3, linking metabolic stress to MICOS disassembly and fission.","evidence":"Competitive Co-IP and T126A site-directed mutagenesis with morphology and apoptosis assays","pmids":["42020360"],"confidence":"Medium","gaps":["Physiological conditions favoring SLC25A6 over CHCHD3 binding undefined","Structural basis of competition unresolved","Single-lab study"]},{"year":2026,"claim":"Reported additional CHCHD3 binding partners (SAMM50, VDAC1/2) coupling its loss to impaired energy metabolism and ROS in lung adenocarcinoma.","evidence":"IP-MS and Co-IP with Seahorse, ROS, cell cycle, and apoptosis assays in LUAD cells","pmids":["42261148"],"confidence":"Low","gaps":["VDAC1/2 interaction validated by a single Co-IP/IP-MS without reciprocal or functional dissection","Direct vs supercomplex-mediated binding to VDAC unclear","Single-lab study"]},{"year":null,"claim":"How the multiple post-translational controls (PKA phosphorylation, Mia40 oxidation, OMA1 cleavage, ASB1/USP3 ubiquitination) are integrated to set CHCHD3 levels and partner choice across physiological states remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No integrated model linking redox, phosphorylation, and ubiquitination states","Functional role of PKA phosphorylation never connected to MICOS/cristae","Structural model of the Sam50-Mic19-Mic60 axis lacking"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0005198","term_label":"structural molecule activity","supporting_discovery_ids":[0,6]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[0,6,8]}],"localization":[{"term_id":"GO:0005739","term_label":"mitochondrion","supporting_discovery_ids":[0,2,4]}],"pathway":[{"term_id":"R-HSA-1852241","term_label":"Organelle biogenesis and maintenance","supporting_discovery_ids":[0,6]},{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[2,5]},{"term_id":"R-HSA-1430728","term_label":"Metabolism","supporting_discovery_ids":[7,8]}],"complexes":["MICOS","MIB supercomplex","Sam50-Mic19-Mic60 axis"],"partners":["MIC60","SAMM50","OPA1","MIA40","OMA1","SLC25A46","VDAC1","USP3"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9NX63","full_name":"MICOS complex subunit MIC19","aliases":["Coiled-coil-helix-coiled-coil-helix domain-containing protein 3"],"length_aa":227,"mass_kda":26.2,"function":"Component of the MICOS complex, a large protein complex of the mitochondrial inner membrane that plays crucial roles in the maintenance of crista junctions, inner membrane architecture, and formation of contact sites to the outer membrane (PubMed:25781180, PubMed:32567732, PubMed:33130824). Plays an important role in the maintenance of the MICOS complex stability and the mitochondrial cristae morphology (PubMed:25781180, PubMed:32567732, PubMed:33130824). Has also been shown to function as a transcription factor which binds to the BAG1 promoter and represses BAG1 transcription (PubMed:22567091)","subcellular_location":"Mitochondrion inner membrane; Cytoplasm; Nucleus; Mitochondrion","url":"https://www.uniprot.org/uniprotkb/Q9NX63/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/CHCHD3","classification":"Not Classified","n_dependent_lines":245,"n_total_lines":1208,"dependency_fraction":0.20281456953642385},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"DNAJC11","stoichiometry":4.0},{"gene":"TOMM20A","stoichiometry":4.0},{"gene":"CAPZB","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/CHCHD3","total_profiled":1310},"omim":[{"mim_id":"616658","title":"MITOCHONDRIAL CONTACT SITE AND CRISTAE ORGANIZING SYSTEM, 13-KD SUBUNIT; MICOS13","url":"https://www.omim.org/entry/616658"},{"mim_id":"615634","title":"COILED-COIL-HELIX-COILED-COIL-HELIX DOMAIN-CONTAINING PROTEIN 6; CHCHD6","url":"https://www.omim.org/entry/615634"},{"mim_id":"613748","title":"COILED-COIL-HELIX-COILED-COIL-HELIX DOMAIN-CONTAINING PROTEIN 3; CHCHD3","url":"https://www.omim.org/entry/613748"},{"mim_id":"612058","title":"SAMM50 SORTING AND ASSEMBLY MACHINERY COMPONENT; SAMM50","url":"https://www.omim.org/entry/612058"},{"mim_id":"608555","title":"METAXIN 2; MTX2","url":"https://www.omim.org/entry/608555"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Mitochondria","reliability":"Supported"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in all","driving_tissues":[{"tissue":"skeletal muscle","ntpm":329.6},{"tissue":"tongue","ntpm":227.3}],"url":"https://www.proteinatlas.org/search/CHCHD3"},"hgnc":{"alias_symbol":["FLJ20420","MINOS3","PPP1R22","Mic19","MICOS19"],"prev_symbol":[]},"alphafold":{"accession":"Q9NX63","domains":[{"cath_id":"1.20.5","chopping":"93-174","consensus_level":"medium","plddt":96.9533,"start":93,"end":174},{"cath_id":"1.10.287","chopping":"183-223","consensus_level":"high","plddt":94.0641,"start":183,"end":223}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9NX63","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9NX63-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9NX63-F1-predicted_aligned_error_v6.png","plddt_mean":84.69},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=CHCHD3","jax_strain_url":"https://www.jax.org/strain/search?query=CHCHD3"},"sequence":{"accession":"Q9NX63","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9NX63.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9NX63/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9NX63"}},"corpus_meta":[{"pmid":"21081504","id":"PMC_21081504","title":"ChChd3, an inner mitochondrial membrane protein, is essential for maintaining crista integrity and mitochondrial function.","date":"2010","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/21081504","citation_count":281,"is_preprint":false},{"pmid":"31097788","id":"PMC_31097788","title":"Sam50-Mic19-Mic60 axis determines mitochondrial cristae architecture by mediating mitochondrial outer and inner membrane contact.","date":"2019","source":"Cell death and differentiation","url":"https://pubmed.ncbi.nlm.nih.gov/31097788","citation_count":92,"is_preprint":false},{"pmid":"38168065","id":"PMC_38168065","title":"Mic19 depletion impairs endoplasmic reticulum-mitochondrial contacts and mitochondrial lipid metabolism and triggers liver disease.","date":"2024","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/38168065","citation_count":71,"is_preprint":false},{"pmid":"23019327","id":"PMC_23019327","title":"Targeting and import mechanism of coiled-coil helix coiled-coil helix domain-containing protein 3 (ChChd3) into the mitochondrial intermembrane space.","date":"2012","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/23019327","citation_count":64,"is_preprint":false},{"pmid":"26416881","id":"PMC_26416881","title":"The Oxidation Status of Mic19 Regulates MICOS Assembly.","date":"2015","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/26416881","citation_count":53,"is_preprint":false},{"pmid":"17242405","id":"PMC_17242405","title":"Identification of ChChd3 as a novel substrate of the cAMP-dependent protein kinase (PKA) using an analog-sensitive catalytic subunit.","date":"2007","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/17242405","citation_count":40,"is_preprint":false},{"pmid":"37473754","id":"PMC_37473754","title":"Liver mitochondrial cristae organizing protein MIC19 promotes energy expenditure and pedestrian locomotion by altering nucleotide metabolism.","date":"2023","source":"Cell metabolism","url":"https://pubmed.ncbi.nlm.nih.gov/37473754","citation_count":26,"is_preprint":false},{"pmid":"30427857","id":"PMC_30427857","title":"Identification and characterization of protein N-myristoylation occurring on four human mitochondrial proteins, SAMM50, TOMM40, MIC19, and MIC25.","date":"2018","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/30427857","citation_count":26,"is_preprint":false},{"pmid":"28808085","id":"PMC_28808085","title":"Sub-mitochondrial localization of the genetic-tagged mitochondrial intermembrane space-bridging components Mic19, Mic60 and Sam50.","date":"2017","source":"Journal of cell science","url":"https://pubmed.ncbi.nlm.nih.gov/28808085","citation_count":26,"is_preprint":false},{"pmid":"22567091","id":"PMC_22567091","title":"Cloning and functional analysis of FLJ20420: a novel transcription factor for the BAG-1 promoter.","date":"2012","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/22567091","citation_count":13,"is_preprint":false},{"pmid":"37511310","id":"PMC_37511310","title":"MIC19 Exerts Neuroprotective Role via Maintaining the Mitochondrial Structure in a Rat Model of Intracerebral Hemorrhage.","date":"2023","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/37511310","citation_count":5,"is_preprint":false},{"pmid":"39113857","id":"PMC_39113857","title":"ASB1 inhibits prostate cancer progression by destabilizing CHCHD3 via K48-linked ubiquitination.","date":"2024","source":"American journal of cancer research","url":"https://pubmed.ncbi.nlm.nih.gov/39113857","citation_count":3,"is_preprint":false},{"pmid":"38350286","id":"PMC_38350286","title":"Up-regulation of MIC19 promotes growth and metastasis of hepatocellular carcinoma by activating ROS/NF-κB signaling.","date":"2024","source":"Translational oncology","url":"https://pubmed.ncbi.nlm.nih.gov/38350286","citation_count":1,"is_preprint":false},{"pmid":"40770539","id":"PMC_40770539","title":"USP3 stabilizes MIC19 by deubiquitination under hypoxic stress and promotes the progression of non-small cell lung cancer.","date":"2025","source":"Acta pharmacologica Sinica","url":"https://pubmed.ncbi.nlm.nih.gov/40770539","citation_count":0,"is_preprint":false},{"pmid":"42261148","id":"PMC_42261148","title":"Targeting CHCHD3 inhibits tumorigenesis of NSCLC by Reprogramming Mitochondrial Metabolism.","date":"2026","source":"Anti-cancer agents in medicinal chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/42261148","citation_count":0,"is_preprint":false},{"pmid":"42020360","id":"PMC_42020360","title":"Glutamine metabolic stress induces SLC25A6-dependent mitofission via MIC60-MIC19 complex disassembly in colorectal cancer.","date":"2026","source":"Cell death & disease","url":"https://pubmed.ncbi.nlm.nih.gov/42020360","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.05.12.653131","title":"DNA-methylation markers associated with lung function at birth and childhood reveal early life programming of inflammatory pathways","date":"2025-05-14","source":"bioRxiv","url":"https://doi.org/10.1101/2025.05.12.653131","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2024.06.20.599846","title":"Age-related MICOS Complex Dysregulation Impairs Mitochondrial 3D Architecture and Metabolic Homeostasis in the Liver","date":"2024-06-25","source":"bioRxiv","url":"https://doi.org/10.1101/2024.06.20.599846","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":11648,"output_tokens":3701,"usd":0.045229,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":11477,"output_tokens":4226,"usd":0.081518,"stage2_stop_reason":"end_turn"},"total_usd":0.126747,"stage1_batch_id":"msgbatch_01ACAxJQabDsht39JXeWG22d","stage2_batch_id":"msgbatch_01QEU22A9U5sbPTgsMzTmvSf","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2010,\n      \"finding\": \"ChChd3 (CHCHD3/Mic19) is a peripheral protein of the mitochondrial inner membrane facing the intermembrane space. RNAi knockdown in HeLa cells caused mitochondrial fragmentation, reduced OPA1 protein levels, impaired fusion, and aberrant cristae with reduced crista junction opening diameter (~50% reduction). ChChd3 interacts with inner membrane proteins mitofilin and OPA1, and outer membrane protein Sam50; knockdown led to near-complete loss of mitofilin and Sam50, establishing ChChd3 as a scaffolding protein stabilizing complexes that maintain crista architecture and protein import.\",\n      \"method\": \"RNAi knockdown in HeLa cells, Co-IP/binding partner analysis, ultrastructural analysis (electron microscopy), oxygen consumption and glycolytic rate measurements\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal binding partner identification, RNAi with defined structural and functional phenotypes, multiple orthogonal methods (EM ultrastructure, biochemistry, metabolic flux), foundational paper replicated by subsequent work\",\n      \"pmids\": [\"21081504\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"CHCHD3 (ChChd3) was identified as a novel substrate of cAMP-dependent protein kinase (PKA) using an analog-sensitive PKA catalytic subunit (M120G mutant) with bulky N6-substituted ATP analogs, establishing PKA as a writer of CHCHD3 phosphorylation.\",\n      \"method\": \"Chemical genetics approach with analog-sensitive PKA catalytic subunit, in vitro kinase assay with N6-substituted ATP analogs, mass spectrometry substrate identification\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — in vitro kinase assay with engineered substrate trapping, single lab, single paper\",\n      \"pmids\": [\"17242405\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"CHCHD3 import into the mitochondrial IMS requires both N-terminal myristoylation and the C-terminal CHCH domain. Myristoylation promotes binding to the outer membrane; the CHCH domain mediates translocation across the outer membrane. The disulfide relay via Mia40 occurs preferentially between Cys193 (second cysteine in helix 1) and Mia40 Cys55. Each of the four CHCH domain cysteines is essential for protein folding and binding to mitofilin and Sam50, but not for import per se.\",\n      \"method\": \"Cysteine mutagenesis, myristoylation site mutagenesis (G2A), in vitro import assays, binding assays to Mia40/mitofilin/Sam50, subcellular fractionation\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — systematic mutagenesis combined with import assays and binding partner analysis, multiple orthogonal methods in single rigorous study\",\n      \"pmids\": [\"23019327\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"MIC19 (CHCHD3) undergoes oxidation in mitochondria and requires the MIA pathway for mitochondrial localization. Yeast Mic19 exists in two redox forms; the intramolecular disulfide-bonded form is specifically bound to Mic60 of the MICOS complex. Mic19 oxidation is not essential for MICOS integration but promotes MICOS assembly and proper inner membrane morphology.\",\n      \"method\": \"Redox state analysis (non-reducing SDS-PAGE), MIA pathway mutant analysis, Co-IP (Mic19-Mic60 interaction), yeast genetics, immunofluorescence\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP, redox biochemistry with multiple genetic and biochemical orthogonal methods, replicated in both human and yeast\",\n      \"pmids\": [\"26416881\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Using genetically encoded tags (miniSOG and APEX2) and electron tomography, Mic19 (CHCHD3) was localized at nanoscale resolution to crista junctions, distributed in a network along the mitochondrial periphery, and enriched inside cristae in cardiac and astrocyte cell lines. Mic19 was found associated with cytochrome c oxidase subunit IV at crista junctions.\",\n      \"method\": \"Genetic tagging with miniSOG and APEX2, electron tomography, subcellular fractionation\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — direct nanoscale structural localization with APEX2/miniSOG and electron tomography, two orthogonal EM tags, two cell lines\",\n      \"pmids\": [\"28808085\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"MIC19 (CHCHD3) is N-myristoylated at its N-terminus. In vitro and in vivo metabolic labeling confirmed N-myristoylation. G2A (non-myristoylated) mutant analysis showed that myristoylation is required for proper mitochondrial targeting and membrane binding of MIC19. Additionally, myristoylation of MIC19 is required for the protein-protein interaction between MIC19 and SAMM50.\",\n      \"method\": \"In vitro and in vivo metabolic labeling with myristate, G2A mutagenesis, immunofluorescence, subcellular fractionation, co-immunoprecipitation\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro and in vivo labeling with mutagenesis and Co-IP, multiple orthogonal methods confirming myristoylation and its functional requirement\",\n      \"pmids\": [\"30427857\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Mic19 (CHCHD3) directly interacts with outer membrane protein Sam50 and inner membrane protein Mic60 to form the Sam50-Mic19-Mic60 axis, which connects SAM and MICOS complexes to assemble the MIB supercomplex and mediates mitochondrial outer-inner membrane contact. OMA1 protease cleaves Mic19 at its N-terminus under physiological stress, disrupting this axis and causing loss of crista junctions, abnormal cristae distribution, and reduced ATP production. Sam50 acts as an anchoring point at the outer membrane guiding crista junction formation.\",\n      \"method\": \"Co-IP, OMA1-mediated cleavage assays, MIB supercomplex analysis, ATP production measurements, mitochondrial morphology analysis, electron microscopy of cristae\",\n      \"journal\": \"Cell death and differentiation\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP, protease cleavage assay, multiple functional readouts (ATP, EM ultrastructure, crista junction morphology), replicated across conditions\",\n      \"pmids\": [\"31097788\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Fasting induces MIC19 (CHCHD3) upregulation in mouse liver, promoting cristae formation. Enforced hepatic MIC19 expression promotes mitochondrial respiration, fatty acid oxidation, and suppresses gluconeogenesis. MIC19-driven cristae formation increases uridine phosphorylase UPP2 activity and uracil accumulation, which signals to promote locomotion.\",\n      \"method\": \"Comparative mouse proteomics, hepatic MIC19 transgenic overexpression, Seahorse respirometry, metabolite profiling, dietary uracil supplementation experiments\",\n      \"journal\": \"Cell metabolism\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vivo transgenic model with multiple metabolic readouts and metabolite profiling, single lab study\",\n      \"pmids\": [\"37473754\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Mic19 (CHCHD3) regulates ER-mitochondria contacts through the EMC2-SLC25A46-Mic19 axis. Liver-specific Mic19 knockout in mice leads to reduction of ER-mitochondrial contacts, mitochondrial lipid metabolism disorder, disorganization of mitochondrial cristae, and mitochondrial unfolded protein stress response in hepatocytes, impairing fatty acid β-oxidation and spontaneously triggering NASH and liver fibrosis. Re-expression of Mic19 in LKO hepatocytes rescued liver disease.\",\n      \"method\": \"Liver-specific conditional knockout (LKO), ER-mitochondria contact site quantification, mitochondrial fractionation, fatty acid oxidation assays, hepatic rescue re-expression experiments, in vivo mouse models\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — conditional KO with rescue experiment, multiple orthogonal functional readouts (ER-mito contacts, lipid metabolism, histology), in vivo model\",\n      \"pmids\": [\"38168065\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"ASB1 E3 ubiquitin ligase interacts with CHCHD3 and promotes its degradation via K48-linked ubiquitination. Loss of ASB1 stabilizes CHCHD3, which activates ROS signaling to promote prostate cancer cell proliferation, clonogenicity, and migration.\",\n      \"method\": \"Quantitative mass spectrometry interactome analysis, co-immunoprecipitation, cycloheximide chase assay, ubiquitination assay, cell rescue experiments\",\n      \"journal\": \"American journal of cancer research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP, ubiquitination assay with K48 linkage specificity, cycloheximide chase, and rescue experiments, single lab\",\n      \"pmids\": [\"39113857\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Under hypoxic conditions, HIF-1α binds the USP3 promoter to upregulate USP3 expression, which in turn stabilizes MIC19 (CHCHD3) through K48-linked deubiquitination, preventing its proteasomal degradation and promoting NSCLC progression.\",\n      \"method\": \"ChIP assay (HIF-1α at USP3 promoter), ubiquitination assay, co-immunoprecipitation (USP3-MIC19), in vitro cell proliferation/invasion assays, in vivo xenograft mouse model\",\n      \"journal\": \"Acta pharmacologica Sinica\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ChIP, Co-IP, ubiquitination assay with deubiquitination specificity, in vivo validation, single lab\",\n      \"pmids\": [\"40770539\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"SLC25A6 directly interacts with MIC60 and competitively inhibits MIC19 (CHCHD3) binding to MIC60, disrupting the MICOS complex. A SLC25A6 T126A mutant failed to bind MIC60, abrogating its ability to destabilize MICOS and cause mitofission. This mechanistically links metabolic stress to mitochondrial fragmentation via displacement of MIC19 from MIC60.\",\n      \"method\": \"Co-immunoprecipitation (SLC25A6-MIC60, competitive with MIC19), site-directed mutagenesis (T126A), mitochondrial morphology analysis, apoptosis assays\",\n      \"journal\": \"Cell death & disease\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP with competitive binding assay and mutagenesis validation, single lab study\",\n      \"pmids\": [\"42020360\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"CHCHD3 knockdown in lung adenocarcinoma cells impaired mitochondrial energy metabolism and caused excessive ROS production. IP-MS and Co-IP validated SAMM50 and VDAC1/2 as direct CHCHD3 binding partners, with disruption of these interactions linked to ROS accumulation.\",\n      \"method\": \"IP-MS, co-immunoprecipitation, Seahorse metabolic analysis, ROS measurement, cell cycle analysis, apoptosis assays\",\n      \"journal\": \"Anti-cancer agents in medicinal chemistry\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single Co-IP/IP-MS validation of binding partners, single lab, limited mechanistic follow-up on VDAC1/2 interaction\",\n      \"pmids\": [\"42261148\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"CHCHD3 (Mic19) is a peripheral mitochondrial inner membrane protein in the IMS that is imported via N-terminal myristoylation and a Mia40-dependent disulfide relay through its CHCH domain; once imported, its oxidized (disulfide-bonded) form associates with Mic60 to nucleate the MICOS complex at crista junctions, where it forms a Sam50-Mic19-Mic60 axis bridging outer and inner membranes to organize cristae architecture, maintain ATP production, and regulate ER-mitochondria contacts for lipid metabolism. Its stability is controlled post-translationally by OMA1-mediated cleavage (disrupting the axis under stress), K48-linked ubiquitination by ASB1 (promoting degradation), and K48-linked deubiquitination by USP3 (stabilizing it under hypoxia downstream of HIF-1α), while PKA-mediated phosphorylation was the original modification identified for this protein.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"CHCHD3 (Mic19) is a peripheral protein of the mitochondrial inner membrane facing the intermembrane space that functions as a scaffolding subunit organizing crista junction architecture and supporting oxidative metabolism [#0]. It is imported into the IMS through a two-signal mechanism: N-terminal myristoylation directs binding to the outer membrane, while its C-terminal CHCH domain mediates translocation and is captured by a Mia40-dependent disulfide relay (Cys193–Mia40 Cys55), and the four CHCH cysteines are required for folding and partner binding rather than import itself [#2, #5]. Once oxidized, the intramolecular disulfide-bonded form selectively engages Mic60 to drive MICOS assembly and proper inner membrane morphology [#3]. CHCHD3 directly bridges the outer-membrane Sam50 and inner-membrane Mic60 to form the Sam50-Mic19-Mic60 axis that unites the SAM and MICOS complexes into the MIB supercomplex and maintains crista junctions and ATP production [#6]; this axis is dismantled when OMA1 cleaves CHCHD3 at its N-terminus under stress [#6] or when SLC25A6 competitively displaces CHCHD3 from Mic60, causing MICOS disruption and mitochondrial fission [#11]. Beyond cristae shaping, CHCHD3 organizes ER-mitochondria contact sites via an EMC2-SLC25A46-Mic19 axis to support mitochondrial lipid metabolism and fatty acid β-oxidation, and hepatic loss spontaneously triggers NASH and liver fibrosis that is reversed by re-expression [#8]. Its abundance is set post-translationally by ASB1-mediated K48 ubiquitination driving degradation and by USP3-mediated K48 deubiquitination that stabilizes it under hypoxia downstream of HIF-1α, with both axes implicated in cancer cell proliferation through ROS signaling [#9, #10].\",\n  \"teleology\": [\n    {\n      \"year\": 2007,\n      \"claim\": \"Before any mitochondrial role was known, CHCHD3 was identified as a phosphorylation substrate, providing the first molecular handle on the protein.\",\n      \"evidence\": \"Chemical-genetic analog-sensitive PKA with N6-substituted ATP analogs and MS substrate identification\",\n      \"pmids\": [\"17242405\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Phosphosite(s) on CHCHD3 not mapped to a function\", \"No link established between PKA phosphorylation and MICOS/cristae roles\", \"Single in vitro study\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Established CHCHD3 as a structural scaffold of the inner membrane whose loss collapses crista architecture and destabilizes import/morphology complexes, defining its core cellular role.\",\n      \"evidence\": \"RNAi in HeLa cells with Co-IP partner mapping, EM ultrastructure, and metabolic flux measurements\",\n      \"pmids\": [\"21081504\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism of how scaffolding stabilizes partners not resolved\", \"Direct vs indirect nature of OPA1 effect unclear\", \"Import-relay details not addressed\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Resolved how CHCHD3 reaches the IMS, separating the myristoylation-dependent membrane-binding step from CHCH-domain-mediated translocation and the Mia40 disulfide relay.\",\n      \"evidence\": \"Cysteine and G2A mutagenesis with in vitro import and Mia40/mitofilin/Sam50 binding assays\",\n      \"pmids\": [\"23019327\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"In vivo myristoyltransferase not identified here\", \"Redox state of mature protein in cells not quantified\", \"How cysteine oxidation gates partner binding unresolved\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Showed that the oxidized, disulfide-bonded form of CHCHD3 is the species that binds Mic60, linking redox state to MICOS assembly competence.\",\n      \"evidence\": \"Non-reducing SDS-PAGE redox analysis, MIA pathway mutants, and reciprocal Co-IP in yeast and human cells\",\n      \"pmids\": [\"26416881\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Stimuli that shift CHCHD3 redox state in vivo unknown\", \"Quantitative contribution of oxidation to morphology not isolated\", \"Reductase/regulators not identified\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Pinpointed CHCHD3 to crista junctions at nanoscale resolution and associated it with respiratory machinery, anchoring its function spatially.\",\n      \"evidence\": \"miniSOG/APEX2 genetic EM tagging and electron tomography in cardiac and astrocyte lines\",\n      \"pmids\": [\"28808085\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Functional consequence of cytochrome c oxidase subunit IV association untested\", \"Dynamics of localization not captured\", \"Cell-type generality beyond two lines unaddressed\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Defined the Sam50-Mic19-Mic60 axis as the physical bridge connecting SAM and MICOS into the MIB supercomplex and showed OMA1 cleavage as a stress-responsive off-switch controlling crista junctions and ATP output.\",\n      \"evidence\": \"Reciprocal Co-IP, OMA1 cleavage assays, MIB supercomplex analysis, ATP and EM cristae readouts\",\n      \"pmids\": [\"31097788\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Trigger and regulation of OMA1 cleavage of CHCHD3 not fully defined\", \"Stoichiometry of the axis unresolved\", \"Structural basis of bridging not determined\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Connected CHCHD3-driven cristae formation to whole-organism physiology, showing fasting-induced upregulation reprograms hepatic respiration and a uracil-UPP2 signaling output.\",\n      \"evidence\": \"Mouse liver proteomics, hepatic transgenic overexpression, respirometry, and metabolite profiling\",\n      \"pmids\": [\"37473754\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism coupling cristae density to UPP2 activity unresolved\", \"Generality beyond liver unknown\", \"Single-lab in vivo model\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Extended CHCHD3 function beyond cristae to ER-mitochondria contact organization via an EMC2-SLC25A46-Mic19 axis required for lipid metabolism, with hepatic loss causing reversible NASH.\",\n      \"evidence\": \"Liver-specific conditional knockout with rescue, contact-site quantification, fatty acid oxidation assays\",\n      \"pmids\": [\"38168065\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular detail of how the axis tethers ER and mitochondria not resolved\", \"Relationship between MICOS and contact-site roles unclear\", \"Direct EMC2/SLC25A46 binding interfaces undefined\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Identified ASB1 as an E3 ligase that destabilizes CHCHD3 via K48 ubiquitination, placing CHCHD3 abundance under proteostatic control with consequences for ROS and tumor cell behavior.\",\n      \"evidence\": \"Interactome MS, Co-IP, cycloheximide chase, ubiquitination and rescue assays in prostate cancer cells\",\n      \"pmids\": [\"39113857\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Ubiquitinated residues on CHCHD3 not mapped\", \"How stabilized CHCHD3 activates ROS signaling unresolved\", \"Single-lab study\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Showed the opposing arm of CHCHD3 proteostasis: hypoxic HIF-1α induces USP3, which deubiquitinates and stabilizes CHCHD3 to promote tumor progression.\",\n      \"evidence\": \"ChIP for HIF-1α at the USP3 promoter, USP3-MIC19 Co-IP, ubiquitination assays, and xenograft model\",\n      \"pmids\": [\"40770539\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Deubiquitination site specificity not mapped\", \"Whether USP3 and ASB1 act on the same lysines unknown\", \"Single-lab study\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Demonstrated a competitive regulatory mechanism in which SLC25A6 binds Mic60 and displaces CHCHD3, linking metabolic stress to MICOS disassembly and fission.\",\n      \"evidence\": \"Competitive Co-IP and T126A site-directed mutagenesis with morphology and apoptosis assays\",\n      \"pmids\": [\"42020360\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Physiological conditions favoring SLC25A6 over CHCHD3 binding undefined\", \"Structural basis of competition unresolved\", \"Single-lab study\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Reported additional CHCHD3 binding partners (SAMM50, VDAC1/2) coupling its loss to impaired energy metabolism and ROS in lung adenocarcinoma.\",\n      \"evidence\": \"IP-MS and Co-IP with Seahorse, ROS, cell cycle, and apoptosis assays in LUAD cells\",\n      \"pmids\": [\"42261148\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"VDAC1/2 interaction validated by a single Co-IP/IP-MS without reciprocal or functional dissection\", \"Direct vs supercomplex-mediated binding to VDAC unclear\", \"Single-lab study\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How the multiple post-translational controls (PKA phosphorylation, Mia40 oxidation, OMA1 cleavage, ASB1/USP3 ubiquitination) are integrated to set CHCHD3 levels and partner choice across physiological states remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No integrated model linking redox, phosphorylation, and ubiquitination states\", \"Functional role of PKA phosphorylation never connected to MICOS/cristae\", \"Structural model of the Sam50-Mic19-Mic60 axis lacking\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [0, 6]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [0, 6, 8]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005758\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0005743\", \"supporting_discovery_ids\": [0, 4]},\n      {\"term_id\": \"GO:0005739\", \"supporting_discovery_ids\": [0, 2, 4]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1852241\", \"supporting_discovery_ids\": [0, 6]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [2, 5]},\n      {\"term_id\": \"R-HSA-1430728\", \"supporting_discovery_ids\": [7, 8]}\n    ],\n    \"complexes\": [\"MICOS\", \"MIB supercomplex\", \"Sam50-Mic19-Mic60 axis\"],\n    \"partners\": [\"MIC60\", \"SAMM50\", \"OPA1\", \"MIA40\", \"OMA1\", \"SLC25A46\", \"VDAC1\", \"USP3\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}