NDUFAF1 (CIA30; Complex I intermediate-associated protein 30, mitochondrial) is a nuclear-encoded mitochondrial assembly factor for respiratory chain complex I (NADH:ubiquinone oxidoreductase). It is the human homologue of the Neurospora crassa complex I chaperone CIA30 and belongs to the CIA30 family, carrying an N-terminal cleavable mitochondrial transit peptide and a galactose-binding domain-like (CIA30/Pfam PF08547) fold. After import, the mature protein is peripherally associated with the matrix face of the mitochondrial inner membrane. NDUFAF1 is a core subunit of the mitochondrial complex I intermediate assembly (MCIA) complex, which additionally contains ACAD9, ECSIT and TMEM126B plus the accessory factors COA1 and TMEM186; within this complex NDUFAF1 binds the N-terminal domain of ECSIT, while ACAD9 binds the ECSIT C-terminal domain, so ECSIT bridges NDUFAF1 and ACAD9. The MCIA complex drives assembly of the membrane arm (ND2-module) of complex I, associating transiently with newly synthesized mtDNA-encoded ND subunits during early intermediate steps and dissociating from the mature holoenzyme. NDUFAF1 is not a structural subunit of complex I and no autonomous catalytic or protein-folding activity has been demonstrated; it acts as a non-catalytic assembly factor. Loss of NDUFAF1 destabilizes the other MCIA components and impairs complex I assembly and activity. Biallelic NDUFAF1 mutations cause mitochondrial complex I deficiency, nuclear type 11 (MC1DN11), presenting as cardioencephalomyopathy / fatal infantile hypertrophic cardiomyopathy. The gene is ubiquitously expressed.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005739 mitochondrion | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: Phylogenetic (IBA) mitochondrial localization. NDUFAF1 is firmly established as a mitochondrial matrix/inner-membrane protein by direct experimental work, so mitochondrion is correct. It is more general than the demonstrated matrix/inner-membrane localization but is not wrong; kept as non-core because the specific location terms below are more informative. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: FB:FBgn0039689 · FB:FBgn0039689 SUPPORTS TRANSFER Experimental descendant seed used by PAINT for the eukaryotic CIA30-family node. PANTHER:PTN000324265 · PANTHER:PTN000324265 NOT RELEVANT Ancestral PAINT node, not a protein donor. The current node-level IBD is GO:0005739 at taxon:2759 in the correct PTHR13194 CIA30 family. UniProtKB:Q9Y375 · UniProtKB:Q9Y375 SUPPORTS TRANSFER NDUFAF1 itself is an expected descendant evidence source; its independent experimental mitochondrial localization makes this non-circular. Supporting Evidence: file:human/NDUFAF1/NDUFAF1-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion |
| GO:0032981 mitochondrial respiratory chain complex I assembly | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic (IBA) annotation to the core biological process of NDUFAF1. This is the central, evolutionarily conserved function of the CIA30 family (Neurospora CIA30 through human NDUFAF1) and is corroborated by multiple direct experimental studies. Accepted as a core function. Propagation Review Root cause: NO FAILURE CORE Sources checked: FB:FBgn0039689 · FB:FBgn0039689 SUPPORTS TRANSFER Experimental descendant seed used to place the conserved assembly-process IBD. PANTHER:PTN000324265 · PANTHER:PTN000324265 NOT RELEVANT Ancestral PAINT node, not a protein donor. The current node-level IBD is GO:0032981 at taxon:2759 in the correct PTHR13194 CIA30 family. UniProtKB:Q9Y375 · UniProtKB:Q9Y375 SUPPORTS TRANSFER The target has direct IMP evidence for complex-I assembly, so its occurrence among the descendant seeds is experimentally grounded rather than circular. WB:WBGene00008225 · WB:WBGene00008225 SUPPORTS TRANSFER Additional experimental descendant seed at the same conserved CIA30-family node. Supporting Evidence: file:human/NDUFAF1/NDUFAF1-uniprot.txt As part of the MCIA complex, involved in the assembly of the |
| GO:0005739 mitochondrion | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: Electronic (UniProtKB-SubCell) mitochondrion annotation, consistent with the UniProt subcellular location and with direct experimental localization data. Correct but general; kept as non-core in favor of the specific matrix / inner-membrane terms. Supporting Evidence: file:human/NDUFAF1/NDUFAF1-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion |
| GO:0005759 mitochondrial matrix | IEA GO_REF:0000044 | ACCEPT | Summary: Electronic (UniProtKB-SubCell) mitochondrial matrix annotation. This matches the UniProt statement that NDUFAF1 localizes to the mitochondrion matrix and is peripherally associated with the matrix face of the inner membrane. Accepted as an accurate, informative location. Supporting Evidence: file:human/NDUFAF1/NDUFAF1-uniprot.txt Mitochondrion matrix |
| GO:0005515 protein binding | IPI PMID:32296183 A reference map of the human binary protein interactome. | KEEP AS NON CORE | Summary: IPI "protein binding" from the HuRI high-throughput binary interactome. The partners captured (PNLIPRP1, SLC30A2, STX8, TMEM86B, TMEM97, YIPF6) are not mitochondrial complex I assembly proteins and are unrelated to NDUFAF1's core function. The IPI nevertheless asserts observed physical interactions and there is no contradictory evidence; retained as non-core rather than used to infer a mechanism. |
| GO:0032981 mitochondrial respiratory chain complex I assembly | IDA PMID:17344420 Cytosolic signaling protein Ecsit also localizes to mitochon... | ACCEPT | Summary: Direct (IDA) annotation to complex I assembly, supported by the demonstration that mitochondrial ECSIT interacts with chaperone NDUFAF1 in 500-850 kDa complexes and that both function in complex I assembly. Consistent with the core function; accepted. Supporting Evidence: PMID:17344420 it interacts with assembly chaperone NDUFAF1 in 500- to 850-kDa complexes |
| GO:0160295 mitochondrial complex I intermediate assembly complex | IDA PMID:33320993 Assembly of The Mitochondrial Complex I Assembly Complex Sug... | ACCEPT | Summary: Direct (IDA) annotation of NDUFAF1 as part of the MCIA complex. The structural study shows NDUFAF1 is a core MCIA subunit that binds ECSIT (with ECSIT bridging NDUFAF1 and ACAD9). Accepted as a core cellular-component annotation. Supporting Evidence: PMID:33320993 The MCIA complex itself is composed of three core subunits—NDUFAF1, ACAD9 and ECSIT |
| GO:0160295 mitochondrial complex I intermediate assembly complex | IDA PMID:34646991 Molecular mechanism of interactions between ACAD9 and bindin... | ACCEPT | Summary: Direct (IDA) annotation of MCIA membership, supported by reconstitution of the ACAD9/ECSIT/NDUFAF1 ternary complex from purified proteins, with NDUFAF1 binding the N-terminal domain of ECSIT. Accepted (duplicate of the MCIA membership annotation with independent supporting evidence). Supporting Evidence: PMID:34646991 ACAD9, ECSIT, and NDUFAF1 interact to form the core mitochondrial CI assembly complex |
| GO:0005739 mitochondrion | IDA GO_REF:0000052 | KEEP AS NON CORE | Summary: Direct (IDA) immunofluorescence-based mitochondrion localization (HPA). Consistent with all other localization evidence. Correct but general; kept as non-core in favor of matrix / inner-membrane terms. Supporting Evidence: file:human/NDUFAF1/NDUFAF1-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion |
| GO:0005743 mitochondrial inner membrane | NAS PMID:32320651 Dissecting the Roles of Mitochondrial Complex I Intermediate... | KEEP AS NON CORE | Summary: Non-traceable (NAS, ComplexPortal) inner-membrane localization. UniProt notes that mature NDUFAF1 is peripherally associated with the matrix face of the mitochondrial inner membrane, so this is biologically appropriate for the membrane-arm assembly role. Kept as non-core (peripheral association; the matrix term is the primary compartment). Supporting Evidence: file:human/NDUFAF1/NDUFAF1-uniprot.txt Peripherally associated with the matrix face of the mitochondrial inner membrane |
| GO:0032981 mitochondrial respiratory chain complex I assembly | NAS PMID:32320651 Dissecting the Roles of Mitochondrial Complex I Intermediate... | ACCEPT | Summary: Non-traceable (NAS, ComplexPortal) annotation to complex I assembly, supported by the MCIA study showing the complex (including NDUFAF1) is required for building the ND2-module of complex I. Consistent with the core function; accepted. Supporting Evidence: PMID:32320651 The mitochondrial complex I intermediate assembly (MCIA) complex, containing assembly factors NDUFAF1, ECSIT, ACAD9, and TMEM126B, is required for building the intermediate ND2-module. |
| GO:0005739 mitochondrion | EXP PMID:17557076 Human CIA30 is involved in the early assembly of mitochondri... | KEEP AS NON CORE | Summary: Experimental (EXP) mitochondrion localization from the study showing CIA30 associates with newly translated mtDNA-encoded complex I subunits at early assembly stages. Correct but general; kept as non-core in favor of the more specific matrix / inner-membrane terms. Supporting Evidence: file:human/NDUFAF1/NDUFAF1-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion |
| GO:0160295 mitochondrial complex I intermediate assembly complex | IDA PMID:32320651 Dissecting the Roles of Mitochondrial Complex I Intermediate... | ACCEPT | Summary: Direct (IDA) annotation of MCIA membership. Formosa et al. define the MCIA complex containing NDUFAF1, ECSIT, ACAD9 and TMEM126B (plus TMEM186 and COA1). Accepted as a core cellular-component annotation. Supporting Evidence: PMID:32320651 The mitochondrial complex I intermediate assembly (MCIA) complex, containing assembly factors NDUFAF1, ECSIT, ACAD9, and TMEM126B |
| GO:0005739 mitochondrion | HTP PMID:34800366 Quantitative high-confidence human mitochondrial proteome an... | KEEP AS NON CORE | Summary: High-throughput (HTP) mitochondrial proteomics localization. Consistent with the well-established mitochondrial localization. Correct but general; kept as non-core in favor of the specific compartment terms. Supporting Evidence: file:human/NDUFAF1/NDUFAF1-uniprot.txt SUBCELLULAR LOCATION: Mitochondrion |
| GO:0005515 protein binding | IPI PMID:33753518 TMEM70 and TMEM242 help to assemble the rotor ring of human ... | KEEP AS NON CORE | Summary: IPI "protein binding" capturing interaction of NDUFAF1 (via the MCIA complex) with TMEM70/TMEM242. The interaction is real and biologically relevant to membrane-arm complex I assembly, but the bare "protein binding" term is uninformative as a mechanistic molecular function. The IPI supports a real physical interaction and is not contradicted, so it is retained as non-core. Supporting Evidence: PMID:33753518 TMEM70 and TMEM242 interact with the mitochondrial complex I assembly (the MCIA) complex that supports assembly of the membrane arm of complex I. |
| GO:0005515 protein binding | IPI PMID:32320651 Dissecting the Roles of Mitochondrial Complex I Intermediate... | KEEP AS NON CORE | Summary: IPI "protein binding" from the MCIA study, capturing NDUFAF1 interactions with other MCIA/complex I components. The exact GOA WITH/FROM includes MT-ND2 (UniProtKB:P03891) as well as MCIA-associated proteins. These interactions are biologically meaningful (MCIA membership is captured better by the GO:0160295 part_of annotations), but the bare "protein binding" MF term is uninformative. The experimental interaction is not contradicted, so the annotation is retained as non-core. |
| GO:0005739 mitochondrion | IDA PMID:16218961 Human mitochondrial complex I assembly is mediated by NDUFAF... | KEEP AS NON CORE | Summary: Direct (IDA) mitochondrion localization from the first study demonstrating NDUFAF1 is a mitochondrial protein involved in complex I assembly. Correct but general; kept as non-core in favor of the specific matrix / inner-membrane terms. Supporting Evidence: PMID:16218961 Here, we demonstrate that NDUFAF1 is a mitochondrial protein that is involved in the complex I assembly process. |
| GO:0032981 mitochondrial respiratory chain complex I assembly | IMP PMID:16218961 Human mitochondrial complex I assembly is mediated by NDUFAF... | ACCEPT | Summary: Direct (IMP) annotation to complex I assembly: RNAi knockdown of NDUFAF1 reduces the amount and activity of complex I, and NDUFAF1 associates with 600/700 kDa assembly intermediates. Strong primary support for the core biological process; accepted. Supporting Evidence: PMID:16218961 Modulating the intramitochondrial amount of NDUFAF1 by knocking down its expression using RNA interference leads to a reduced amount and activity of complex I. |
| GO:0005743 mitochondrial inner membrane | TAS Reactome:R-HSA-6799179 | KEEP AS NON CORE | Summary: Traceable (TAS, Reactome) inner-membrane localization within the complex I biogenesis pathway. Consistent with NDUFAF1's peripheral association with the matrix face of the inner membrane during assembly. Kept as non-core. Supporting Evidence: file:human/NDUFAF1/NDUFAF1-uniprot.txt Peripherally associated with the matrix face of the mitochondrial inner membrane |
| GO:0005743 mitochondrial inner membrane | TAS Reactome:R-HSA-6799196 | KEEP AS NON CORE | Summary: Traceable (TAS, Reactome) inner-membrane localization, from the pathway step in which the MCIA complex dissociates from the maturing complex I. Consistent with peripheral inner-membrane association during assembly. Kept as non-core. Supporting Evidence: file:human/NDUFAF1/NDUFAF1-uniprot.txt Peripherally associated with the matrix face of the mitochondrial inner membrane |
| GO:0005743 mitochondrial inner membrane | TAS Reactome:R-HSA-6799197 | KEEP AS NON CORE | Summary: Traceable (TAS, Reactome) inner-membrane localization within the complex I biogenesis pathway. Consistent with the peripheral inner-membrane association of NDUFAF1 during membrane-arm assembly. Kept as non-core. Supporting Evidence: file:human/NDUFAF1/NDUFAF1-uniprot.txt Peripherally associated with the matrix face of the mitochondrial inner membrane |
| GO:0005743 mitochondrial inner membrane | TAS Reactome:R-HSA-6799199 | KEEP AS NON CORE | Summary: Traceable (TAS, Reactome) inner-membrane localization from the step in which COA1:MT-ND2, TMEM186:MT-ND3, MT-ND6 and NDUFB6 bind the MCIA complex. Consistent with peripheral inner-membrane association during assembly. Kept as non-core. Supporting Evidence: file:human/NDUFAF1/NDUFAF1-uniprot.txt Peripherally associated with the matrix face of the mitochondrial inner membrane |
| GO:0005743 mitochondrial inner membrane | TAS Reactome:R-HSA-6799202 | KEEP AS NON CORE | Summary: Traceable (TAS, Reactome) inner-membrane localization within the complex I biogenesis pathway. Consistent with peripheral inner-membrane association of NDUFAF1 during assembly. Kept as non-core. Supporting Evidence: file:human/NDUFAF1/NDUFAF1-uniprot.txt Peripherally associated with the matrix face of the mitochondrial inner membrane |
| GO:0005515 protein binding | IPI PMID:20816094 Acyl-CoA dehydrogenase 9 is required for the biogenesis of o... | KEEP AS NON CORE | Summary: IPI "protein binding" capturing the NDUFAF1-ACAD9 interaction. This is a biologically important MCIA interaction, but the interaction is better represented by the MCIA complex membership (GO:0160295), and the bare "protein binding" MF term is uninformative. The IPI remains valid evidence of physical interaction and is retained as non-core. Supporting Evidence: PMID:20816094 ACAD9 binds complex I assembly factors NDUFAF1 and Ecsit and is specifically required for the assembly of complex I. |
| GO:0005515 protein binding | IPI PMID:17344420 Cytosolic signaling protein Ecsit also localizes to mitochon... | KEEP AS NON CORE | Summary: IPI "protein binding" capturing the NDUFAF1-ECSIT interaction. Real and central to MCIA architecture (NDUFAF1 binds the N-terminal domain of ECSIT), but MCIA membership (GO:0160295) is the informative representation, and the bare "protein binding" MF term is uninformative. The observed interaction is not contradicted and is therefore retained as non-core. Supporting Evidence: PMID:17344420 it interacts with chaperone NDUFAF1 |
| GO:0006120 mitochondrial electron transport, NADH to ubiquinone | NAS PMID:11935339 CIA30 complex I assembly factor: a candidate for human compl... | MARK AS OVER ANNOTATED | Summary: NAS annotation to the complex I catalytic process (electron transport, NADH to ubiquinone). NDUFAF1 is an assembly factor that is NOT a structural subunit of complex I and has no role in electron transport itself; it dissociates from the mature holoenzyme. This is an over-annotation conflating the assembly factor with the enzymatic process it enables. The accurate process is complex I assembly (GO:0032981), which is already annotated. Marked as over-annotated (NAS, from the original candidate-gene paper). |
| GO:0065003 protein-containing complex assembly | NAS PMID:11935339 CIA30 complex I assembly factor: a candidate for human compl... | MODIFY | Summary: NAS annotation to the general process "protein-containing complex assembly." This is correct in spirit (NDUFAF1 is a chaperone-like assembly factor) but far more general than the specific, well-supported term mitochondrial respiratory chain complex I assembly (GO:0032981). Modify to the specific complex I assembly term. Proposed replacements: mitochondrial respiratory chain complex I assembly Supporting Evidence: file:human/NDUFAF1/NDUFAF1-uniprot.txt As part of the MCIA complex, involved in the assembly of the |
| GO:0051082 unfolded protein binding | IBA GO_REF:0000033 | MARK AS OVER ANNOTATED | Summary: Separately reviewed legacy propagated claim retained in the UniProt record as `IBA:GO_Central`; it is not one of the 27 current GOA signatures. GO:0051082 is now obsolete, and neither the current PAINT slice nor the NDUFAF1 literature supports direct binding to an unfolded client. Association with newly translated complex-I subunits during assembly does not establish their conformational state or an autonomous chaperone molecular function. Reason: The assembly-factor biology is real, but this propagated molecular-function claim over-interprets “assembly chaperone” as unfolded-protein binding. Current PAINT for PTHR13194/PTN000324265 contains only GO:0005739 and GO:0032981 IBDs. GO:0044183 is not justified because autonomous folding was not assayed, and carrier-specific GO:0140309 is not justified because client escort was not shown. Propagation Review Root cause: SOURCE STALE OR MISSING Failure modes: SOURCE EVIDENCE WEAK Sources checked: PANTHER:PTN000324265 · PANTHER:PTN000324265 SOURCE STALE OR MISSING The retained current PAINT slice for PTHR13194 contains exactly two IBDs at this node, GO:0005739 and GO:0032981; GO:0051082 is absent. This classifies a stale historical transfer and does not challenge either current node placement. UniProtKB:Q9Y375 · UniProtKB:Q9Y375 SOURCE WEAK OR INFERRED The UniProt flat file still preserves `F:unfolded protein binding; IBA:GO_Central`, but this is an inferred legacy cross-reference rather than independent experimental evidence for unfolded-client recognition. Supporting Evidence: file:human/NDUFAF1/NDUFAF1-uniprot.txt F:unfolded protein binding; IBA:GO_Central. PMID:17557076 human complex I assembly factor CIA30 (complex I intermediate associated protein) associates with newly translated mtDNA-encoded complex I subunits at early stages in their assembly before dissociating at a later stage. |
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Download this section (compressed HTML)Q: Which complex-I subunit or assembly-intermediate surfaces contact NDUFAF1 directly, and does NDUFAF1 stabilize those contacts without recognizing an unfolded state?
Experiment: Reconstitute defined MCIA intermediates with purified NDUFAF1 and map direct contacts by cross-linking mass spectrometry and cryo-EM; compare wild-type and interface mutants in NDUFAF1-null cells, while separately assaying generic unfolded-protein binding and refolding to distinguish assembly scaffolding from chaperone activity.
Hypothesis: NDUFAF1 promotes ND2-module assembly through specific MCIA and nascent-subunit contacts rather than through autonomous foldase or unfolded-protein-binding activity.
Type: biochemical reconstitution, structural mapping, and genetic rescue
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