Affinage

CHCHD3

MICOS complex subunit MIC19 · UniProt Q9NX63

Round 2 corrected
Length
227 aa
Mass
26.2 kDa
Annotated
2026-04-28
45 papers in source corpus 9 papers cited in narrative 9 extracted findings

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

CHCHD3 (MIC19) is a peripheral mitochondrial inner membrane protein of the intermembrane space that functions as a central scaffolding subunit of the MICOS complex, organizing crista junction architecture and bridging the outer and inner mitochondrial membranes. It forms the Sam50–Mic19–Mic60 axis that assembles the MIB supercomplex; OMA1-mediated cleavage of its N-terminus disassembles this axis, ablating crista junctions and reducing ATP production (PMID:31097788). Import into the intermembrane space requires both N-terminal myristoylation—necessary for outer membrane binding and interaction with Sam50—and CHCH domain twin CX9C motifs that engage the Mia40 disulfide relay (PMID:23019327, PMID:30427857). CHCHD3 protein stability is regulated by K48-linked ubiquitination promoted by the E3 ligase adaptor ASB1 and by deubiquitination mediated by USP3, the latter induced by HIF-1α under hypoxia (PMID:39113857, PMID:40770539).

Mechanistic history

Synthesis pass · year-by-year structured walk · 9 steps
  1. 2007 Medium

    Identifying CHCHD3 as a PKA substrate placed this previously uncharacterized CHCH-domain protein in a signaling context and marked it as a mitochondrial phosphoprotein.

    Evidence Chemical genetics with analog-sensitive PKA and mass spectrometry identification

    PMID:17242405

    Open questions at the time
    • Phosphorylation site(s) and functional consequences of PKA phosphorylation on CHCHD3 were not determined
    • No independent confirmation of CHCHD3 as an in vivo PKA substrate
  2. 2010 High

    RNAi studies established CHCHD3 as essential for crista integrity, revealing that it scaffolds mitofilin (Mic60), OPA1, and Sam50 at the inner membrane and that its loss causes crista fragmentation, reduced crista junction diameter, mitochondrial fragmentation, and impaired respiration.

    Evidence RNAi in HeLa cells combined with co-immunoprecipitation, electron tomography, and metabolic flux measurements

    PMID:21081504

    Open questions at the time
    • Whether CHCHD3 contacts Sam50 and Mic60 simultaneously or sequentially was not resolved
    • Mechanism by which CHCHD3 loss reduces OPA1 levels was not determined
  3. 2012 High

    Systematic mutagenesis delineated a dual import mechanism: N-terminal myristoylation drives outer membrane association while the CHCH domain engages the Mia40 oxidative relay for intermembrane space translocation, with distinct roles for individual CX9C cysteines in folding versus import.

    Evidence Mutagenesis of G2 (myristoylation) and all four CHCH cysteines; subcellular fractionation; Mia40 co-immunoprecipitation

    PMID:23019327

    Open questions at the time
    • Kinetics and order of disulfide bond formation in vivo were not resolved
    • Whether additional chaperones assist CHCHD3 folding after Mia40 engagement is unknown
  4. 2017 High

    Nanoscale electron tomography pinpointed CHCHD3 to crista junctions in a peripheral network pattern, directly confirming the structural predictions from loss-of-function studies.

    Evidence miniSOG and APEX2 genetic tags with electron tomography in mouse cardiac and human astrocyte cells

    PMID:28808085

    Open questions at the time
    • Functional significance of the observed CHCHD3–cytochrome c oxidase subunit IV association remains unexplored
    • Whether crista junction enrichment changes under metabolic stress is unknown
  5. 2018 High

    Independent validation confirmed that N-myristoylation is essential for mitochondrial targeting and for the CHCHD3–Sam50 interaction, consolidating myristoylation as the obligate first step in CHCHD3 membrane engagement.

    Evidence Metabolic labeling, immunofluorescence, subcellular fractionation, and Co-IP with G2A mutant

    PMID:30427857

    Open questions at the time
    • Whether myristoylation is constitutive or regulated remains unaddressed
  6. 2019 High

    Defining the Sam50–Mic19–Mic60 axis as the bridge between the SAM and MICOS complexes explained how CHCHD3 couples outer and inner membrane organization; OMA1-mediated cleavage of CHCHD3's N-terminus was identified as a mechanism to disassemble this axis and remodel cristae.

    Evidence Co-immunoprecipitation, OMA1 cleavage assays, electron microscopy, and ATP production measurements

    PMID:31097788

    Open questions at the time
    • Signals that activate OMA1 cleavage of CHCHD3 specifically are not fully characterized
    • Stoichiometry of the Sam50–Mic19–Mic60 axis within a single crista junction is unknown
  7. 2024 Medium

    Identification of ASB1-mediated K48-linked ubiquitination as a degradation pathway for CHCHD3 revealed a post-translational mechanism controlling its protein levels, linking CHCHD3 turnover to ROS-dependent cancer cell proliferation.

    Evidence Quantitative MS interactome, Co-IP, cycloheximide chase, ubiquitination assays, and cell rescue in prostate cancer cells

    PMID:39113857

    Open questions at the time
    • The specific ubiquitination site(s) on CHCHD3 were not mapped
    • Relevance of ASB1–CHCHD3 regulation outside prostate cancer cells is untested
  8. 2025 Medium

    USP3 was identified as the deubiquitinase counteracting K48-linked ubiquitination of CHCHD3, stabilizing it under hypoxia via HIF-1α–driven USP3 transcription and thereby promoting NSCLC progression.

    Evidence ChIP for HIF-1α at USP3 promoter; USP3 knockdown/overexpression; deubiquitination assays; in vivo NSCLC models

    PMID:40770539

    Open questions at the time
    • Whether USP3 directly deubiquitinates CHCHD3 or acts through an intermediary was not biochemically demonstrated with purified components
    • Interplay between OMA1 cleavage and ubiquitin-dependent degradation is unexplored
  9. 2026 Medium

    SLC25A6 was shown to competitively displace CHCHD3 from Mic60, providing the first evidence that MICOS integrity is regulated by a metabolite transporter competing for the same binding interface on Mic60.

    Evidence Co-IP, competitive binding assays, T126A mutagenesis, mitochondrial morphology imaging

    PMID:42020360

    Open questions at the time
    • Structural basis of SLC25A6–MIC60 versus MIC19–MIC60 competition is unresolved
    • Physiological conditions under which SLC25A6 displaces MIC19 in vivo remain undefined

Open questions

Synthesis pass · forward-looking unresolved questions
  • Key unresolved questions include the structural basis of the Sam50–Mic19–Mic60 bridging complex at atomic resolution, the functional role of PKA phosphorylation on CHCHD3, and how OMA1 cleavage and ubiquitin-dependent degradation pathways are coordinated to regulate CHCHD3 levels during stress.
  • No high-resolution structure of CHCHD3 in complex with Mic60 or Sam50 exists
  • Functional consequence of PKA-mediated phosphorylation remains unknown
  • Crosstalk between OMA1 proteolysis and ASB1/USP3 ubiquitin regulation has not been examined

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0005198 structural molecule activity 2 GO:0060090 molecular adaptor activity 2
Localization
GO:0005739 mitochondrion 5
Pathway
R-HSA-1852241 Organelle biogenesis and maintenance 3 R-HSA-1430728 Metabolism 2
Partners
ASB1MIA40MIC60OMA1OPA1SAM50SLC25A6USP3
Complex memberships
MIB (mitochondrial intermembrane space bridging) supercomplexMICOS complex

Evidence

Reading pass · 9 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2007 CHCHD3 (ChChd3) was identified as a novel substrate of cAMP-dependent protein kinase (PKA) using an analog-sensitive catalytic subunit chemical genetics approach, establishing it as a PKA-phosphorylated mitochondrial protein. Chemical genetics with analog-sensitive PKA catalytic subunit (M120G mutant) and N6-substituted ATP analogs; mass spectrometry identification The Journal of biological chemistry Medium 17242405
2010 CHCHD3 (ChChd3) is a peripheral protein of the mitochondrial inner membrane facing the intermembrane space that is essential for maintaining crista integrity. RNAi knockdown causes mitochondrial fragmentation, reduced OPA1 protein levels and impaired fusion, clustering of mitochondria around the nucleus, and severely restricted oxygen consumption and glycolytic rates. Ultrastructural analysis revealed aberrant cristae with fragmented/tubular structures and 50% reduction in crista junction opening diameter. CHCHD3 interacts with inner membrane proteins mitofilin and OPA1 (which regulate crista morphology) and outer membrane protein Sam50 (regulating β-barrel protein import); knockdown causes near-complete loss of both mitofilin and Sam50, indicating CHCHD3 is a scaffolding protein stabilizing protein complexes involved in crista architecture and protein import. RNAi knockdown in HeLa cells; co-immunoprecipitation; electron tomography/ultrastructural analysis; oxygen consumption and glycolytic rate measurements; immunoblotting The Journal of biological chemistry High 21081504
2012 CHCHD3 import into the mitochondrial intermembrane space requires both N-terminal myristoylation (which promotes binding to the outer membrane) and the CHCH domain with twin CX9C motifs (which translocates the protein across the outer membrane). The CHCH domain cysteines have distinct roles: a transient disulfide-bonded intermediate with Mia40 is formed preferentially between Cys193 (second cysteine in helix 1) and the active site Cys55 of Mia40. All four cysteines are essential for protein folding and binding to mitofilin and Sam50 but are not required for import per se. Systematic mutagenesis of myristoylation site (G2A) and CHCH domain cysteines; subcellular fractionation; co-immunoprecipitation with Mia40; import assays The Journal of biological chemistry High 23019327
2017 Nanoscale electron tomography using miniSOG and APEX2 genetic tags showed that CHCHD3 (Mic19) localizes specifically at crista junctions, distributed in a network pattern along the mitochondrial periphery and enriched inside cristae, in both mouse cardiac and human astrocyte cell lines. An association of CHCHD3/Mic19 with cytochrome c oxidase subunit IV was also discovered. Electron tomography with miniSOG and APEX2 genetic tags; co-immunoprecipitation; sub-mitochondrial localization mapping Journal of cell science High 28808085
2018 CHCHD3 (MIC19) undergoes N-myristoylation at its N-terminus, and this lipid modification is required for proper mitochondrial targeting and membrane binding. Non-myristoylated G2A mutant MIC19 fails to localize to mitochondria. N-myristoylation of MIC19 is also required for its interaction with SAMM50 (Sam50), as demonstrated by immunoprecipitation with a stable MIC19 transformant. In vitro and in vivo metabolic labeling; immunofluorescence microscopy; subcellular fractionation; immunoprecipitation with G2A mutants PloS one High 30427857
2019 CHCHD3 (Mic19) directly interacts with the mitochondrial outer-membrane protein Sam50 and inner-membrane protein Mic60 to form the Sam50-Mic19-Mic60 axis, which connects the SAM and MICOS complexes to assemble the MIB (mitochondrial intermembrane space bridging) supercomplex for mediating mitochondrial outer- and inner-membrane contact. OMA1-mediated cleavage of Mic19 at its N-terminus disrupts this axis, separating SAM and MICOS and leading to MIB disassembly, abnormal mitochondrial morphology, loss of crista junctions, and reduced ATP production. Co-immunoprecipitation; genetic disruption of Sam50-Mic19-Mic60 axis; OMA1 cleavage assays; ATP production measurements; electron microscopy of crista junctions Cell death and differentiation High 31097788
2024 ASB1 (Ankyrin Repeat and SOCS Box Containing 1) interacts with CHCHD3 and promotes its degradation via K48-linked ubiquitination, destabilizing CHCHD3 protein levels. ASB1-mediated suppression of CHCHD3 inhibits prostate cancer cell proliferation, clonogenicity, and migration through the CHCHD3/ROS pathway. Quantitative mass spectrometry interactome; co-immunoprecipitation; cycloheximide chase; ubiquitination assays; cell rescue experiments American journal of cancer research Medium 39113857
2025 Under hypoxic conditions, HIF-1α binds the USP3 promoter to upregulate USP3 expression, which in turn stabilizes CHCHD3 (MIC19) through K48-linked deubiquitination, preventing its degradation and driving NSCLC progression. ChIP assay for HIF-1α binding; USP3 knockdown/overexpression; ubiquitination and deubiquitination assays; in vitro and in vivo NSCLC models Acta pharmacologica Sinica Medium 40770539
2026 SLC25A6 directly interacts with MIC60 and competitively inhibits CHCHD3 (MIC19) binding to MIC60, disrupting the MICOS complex and inducing mitochondrial fragmentation. The SLC25A6 T126A mutant fails to bind MIC60 and cannot destabilize the MICOS complex, demonstrating that the SLC25A6-MIC60 interaction specifically displaces MIC19 from MICOS. Co-immunoprecipitation; competitive binding assays; site-directed mutagenesis (T126A); mitochondrial morphology imaging; apoptosis assays Cell death & disease Medium 42020360

Source papers

Stage 0 corpus · 45 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2005 Towards a proteome-scale map of the human protein-protein interaction network. Nature 2090 16189514
2002 Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proceedings of the National Academy of Sciences of the United States of America 1479 12477932
2016 ATPase-Modulated Stress Granules Contain a Diverse Proteome and Substructure. Cell 1233 26777405
2017 Architecture of the human interactome defines protein communities and disease networks. Nature 1085 28514442
2015 A human interactome in three quantitative dimensions organized by stoichiometries and abundances. Cell 1015 26496610
2014 A proteome-scale map of the human interactome network. Cell 977 25416956
2020 A reference map of the human binary protein interactome. Nature 849 32296183
2018 VIRMA mediates preferential m6A mRNA methylation in 3'UTR and near stop codon and associates with alternative polyadenylation. Cell discovery 829 29507755
2003 Complete sequencing and characterization of 21,243 full-length human cDNAs. Nature genetics 754 14702039
2021 Dual proteome-scale networks reveal cell-specific remodeling of the human interactome. Cell 705 33961781
2012 A census of human soluble protein complexes. Cell 689 22939629
2011 Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Briefings in bioinformatics 656 21873635
2008 Large-scale proteomics and phosphoproteomics of urinary exosomes. Journal of the American Society of Nephrology : JASN 607 19056867
2004 The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome research 438 15489334
2022 OpenCell: Endogenous tagging for the cartography of human cellular organization. Science (New York, N.Y.) 432 35271311
2010 Systematic analysis of human protein complexes identifies chromosome segregation proteins. Science (New York, N.Y.) 421 20360068
2015 Panorama of ancient metazoan macromolecular complexes. Nature 407 26344197
2021 A proximity-dependent biotinylation map of a human cell. Nature 339 34079125
2012 Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins. Nature 319 22810586
2019 Mitochondrial ClpP-Mediated Proteolysis Induces Selective Cancer Cell Lethality. Cancer cell 298 31056398
2006 Phosphoproteome analysis of the human mitotic spindle. Proceedings of the National Academy of Sciences of the United States of America 281 16565220
2010 ChChd3, an inner mitochondrial membrane protein, is essential for maintaining crista integrity and mitochondrial function. The Journal of biological chemistry 275 21081504
2009 Docking motif-guided mapping of the interactome of protein phosphatase-1. Chemistry & biology 269 19389623
2011 A directed protein interaction network for investigating intracellular signal transduction. Science signaling 258 21900206
2021 Quantitative high-confidence human mitochondrial proteome and its dynamics in cellular context. Cell metabolism 239 34800366
2013 The functional interactome landscape of the human histone deacetylase family. Molecular systems biology 235 23752268
2007 hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes. Genomics 222 17207965
2016 Mitochondrial Protein Interaction Mapping Identifies Regulators of Respiratory Chain Function. Molecular cell 220 27499296
2016 An organelle-specific protein landscape identifies novel diseases and molecular mechanisms. Nature communications 211 27173435
2018 An AP-MS- and BioID-compatible MAC-tag enables comprehensive mapping of protein interactions and subcellular localizations. Nature communications 201 29568061
2011 Next-generation sequencing to generate interactome datasets. Nature methods 200 21516116
2019 Sam50-Mic19-Mic60 axis determines mitochondrial cristae architecture by mediating mitochondrial outer and inner membrane contact. Cell death and differentiation 87 31097788
2024 Mic19 depletion impairs endoplasmic reticulum-mitochondrial contacts and mitochondrial lipid metabolism and triggers liver disease. Nature communications 64 38168065
2012 Targeting and import mechanism of coiled-coil helix coiled-coil helix domain-containing protein 3 (ChChd3) into the mitochondrial intermembrane space. The Journal of biological chemistry 63 23019327
2015 The Oxidation Status of Mic19 Regulates MICOS Assembly. Molecular and cellular biology 50 26416881
2007 Identification of ChChd3 as a novel substrate of the cAMP-dependent protein kinase (PKA) using an analog-sensitive catalytic subunit. The Journal of biological chemistry 40 17242405
2023 Liver mitochondrial cristae organizing protein MIC19 promotes energy expenditure and pedestrian locomotion by altering nucleotide metabolism. Cell metabolism 26 37473754
2017 Sub-mitochondrial localization of the genetic-tagged mitochondrial intermembrane space-bridging components Mic19, Mic60 and Sam50. Journal of cell science 26 28808085
2018 Identification and characterization of protein N-myristoylation occurring on four human mitochondrial proteins, SAMM50, TOMM40, MIC19, and MIC25. PloS one 25 30427857
2012 Cloning and functional analysis of FLJ20420: a novel transcription factor for the BAG-1 promoter. PloS one 13 22567091
2023 MIC19 Exerts Neuroprotective Role via Maintaining the Mitochondrial Structure in a Rat Model of Intracerebral Hemorrhage. International journal of molecular sciences 5 37511310
2024 ASB1 inhibits prostate cancer progression by destabilizing CHCHD3 via K48-linked ubiquitination. American journal of cancer research 3 39113857
2024 Up-regulation of MIC19 promotes growth and metastasis of hepatocellular carcinoma by activating ROS/NF-κB signaling. Translational oncology 1 38350286
2026 Glutamine metabolic stress induces SLC25A6-dependent mitofission via MIC60-MIC19 complex disassembly in colorectal cancer. Cell death & disease 0 42020360
2025 USP3 stabilizes MIC19 by deubiquitination under hypoxic stress and promotes the progression of non-small cell lung cancer. Acta pharmacologica Sinica 0 40770539