NDUFS6 (NADH:ubiquinone oxidoreductase subunit S6; also called the "13 kDa-A" or CI-13kD-A subunit) is a small (124-residue precursor; ~13 kDa) nuclear-encoded accessory (supernumerary) subunit of mitochondrial respiratory Complex I (NADH:ubiquinone oxidoreductase). It carries an N-terminal mitochondrial transit peptide (residues 1-28) and a C-terminal CHCC-type zinc-binding motif (zf-CHCC). Within the L-shaped holoenzyme it is part of the peripheral (matrix) arm, near the flavoprotein/NADH-oxidising N-module, and it was historically grouped with the iron-sulfur protein (IP) fraction. Despite the "S" (iron-sulfur protein) name it is a non-catalytic subunit that does not carry an electron-transfer Fe-S cluster of the catalytic wire; instead it plays a structural role, stabilising the N-module during Complex I assembly. It is a peripheral inner-membrane protein on the matrix side of the mitochondrial inner membrane. Complex I couples electron transfer from NADH to ubiquinone with proton translocation across the inner membrane, feeding the respiratory chain and driving oxidative phosphorylation. Loss-of-function variants in NDUFS6 destabilise Complex I and cause mitochondrial complex I deficiency (nuclear type 9, MC1DN9), presenting as fatal neonatal lactic acidosis and Leigh-like encephalopathy.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005743 mitochondrial inner membrane | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic (IBA) placement of NDUFS6 at the mitochondrial inner membrane, the site of Complex I. Consistent with UniProt subcellular location and direct evidence; this is the correct anatomical location for the subunit. Reason: NDUFS6 is a peripheral inner-membrane subunit of Complex I, which resides in the mitochondrial inner membrane. The IBA is well supported by the UniProt curated location and by direct localisation evidence (PMID:28844695). Supporting Evidence: file:human/NDUFS6/NDUFS6-uniprot.txt Mitochondrion inner membrane |
| GO:0006120 mitochondrial electron transport, NADH to ubiquinone | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic (IBA) involvement in mitochondrial electron transport from NADH to ubiquinone, the core process carried out by Complex I. NDUFS6 contributes to this process as an accessory subunit required for assembly/stability of the functional holoenzyme, even though it is not itself catalytic. Reason: This is the core biological process of the complex NDUFS6 belongs to. The involved_in qualifier is appropriate for a subunit that is part of the machine performing NADH-> ubiquinone electron transport. Well supported across the phylogeny and by the complex's characterised catalytic function. Supporting Evidence: PMID:9878551 Its main function is the transport of electrons from NADH to ubiquinone, which is accompanied by translocation of protons from the mitochondrial matrix to the intermembrane space. |
| GO:0045271 respiratory chain complex I | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic (IBA) assignment of NDUFS6 as part_of respiratory chain complex I. This is the central, well-established membership for this protein and is the preferred (non-obsolete) complex term. Reason: NDUFS6 is an integral accessory subunit of Complex I, supported by IBA and by multiple direct/experimental annotations (PMID:12611891, PMID:27626371, PMID:28844695). GO:0045271 is the correct, current complex term. Supporting Evidence: PMID:12611891 we can resolve and identify the human homologues of 42 polypeptides detected so far in the more extensively studied beef heart complex I |
| GO:0005739 mitochondrion | IEA GO_REF:0000117 | KEEP AS NON CORE | Summary: Electronic (ARBA) localisation to the mitochondrion. Correct but non-specific: NDUFS6 localises more precisely to the mitochondrial inner membrane. Reason: The mitochondrion annotation is true but is a broad parent of the more informative mitochondrial inner membrane term (GO:0005743) that is separately annotated. Retained as non-core rather than removed, since it is not wrong. Supporting Evidence: file:human/NDUFS6/NDUFS6-uniprot.txt Mitochondrion inner membrane |
| GO:0005743 mitochondrial inner membrane | IEA GO_REF:0000120 | ACCEPT | Summary: Electronic (combined IEA) localisation to the mitochondrial inner membrane. Matches the curated UniProt location and direct evidence; this is the correct specific anatomical location. Reason: NDUFS6 is a peripheral inner-membrane subunit of Complex I on the matrix side of the inner membrane, consistent with the UniProt curated subcellular location. Supporting Evidence: file:human/NDUFS6/NDUFS6-uniprot.txt Peripheral membrane protein |
| GO:0006120 mitochondrial electron transport, NADH to ubiquinone | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO (IEA) involvement in NADH-to-ubiquinone electron transport, mapped from the NDUFS6 InterPro signature (IPR016668). Consistent with the IBA and with the core process of Complex I. Reason: This IEA duplicates the well-supported core process annotation and is at the correct level of specificity for a Complex I subunit. Supporting Evidence: PMID:9878551 Its main function is the transport of electrons from NADH to ubiquinone |
| GO:1902600 proton transmembrane transport | IEA GO_REF:0000108 | MARK AS OVER ANNOTATED | Summary: Automatically inferred (GO_REF:0000108, from GO:0008137 NADH dehydrogenase activity) involvement in proton transmembrane transport. Complex I as a whole pumps protons, but NDUFS6 is a small peripheral-arm accessory subunit near the N-module, not part of the membrane-arm proton-pumping machinery. Reason: Proton translocation is a complex-level activity performed by the membrane (HP) arm antiporter-like subunits (ND2/ND4/ND5 etc.), not by this matrix-side accessory subunit. The annotation is a logical propagation from the (also over-annotated) NADH dehydrogenase activity term and over-reaches for NDUFS6 as an individual subunit. Supporting Evidence: file:human/NDUFS6/NDUFS6-uniprot.txt Accessory subunit of the mitochondrial membrane respiratory |
| GO:0045271 respiratory chain complex I | IEA GO_REF:0000120 | ACCEPT | Summary: Electronic (combined IEA) assignment as part_of respiratory chain complex I. Duplicates the strongly supported complex membership. Reason: Correct and consistent with IBA and multiple experimental annotations of Complex I membership. Supporting Evidence: file:human/NDUFS6/NDUFS6-uniprot.txt Accessory subunit of the mitochondrial membrane respiratory |
| GO:0005743 mitochondrial inner membrane | IDA PMID:28844695 Architecture of Human Mitochondrial Respiratory Megacomplex ... | ACCEPT | Summary: Direct (IDA, ComplexPortal) localisation of NDUFS6 to the mitochondrial inner membrane, based on the cryo-EM structure of the human respiratory megacomplex in which the precise subunit assignments of Complex I were determined. Reason: The cryo-EM megacomplex structure resolves individual Complex I subunits, placing NDUFS6 within the inner-membrane-embedded holoenzyme. This is the correct anatomical location. Supporting Evidence: PMID:28844695 reveals the precise assignment of individual subunits of human CI and CIII |
| GO:0009060 aerobic respiration | NAS PMID:30030361 Assembly of mammalian oxidative phosphorylation complexes I-... | KEEP AS NON CORE | Summary: Author-stated (NAS, ComplexPortal) involvement in aerobic respiration. True at the level of the OXPHOS system that Complex I feeds, but a high-level, non-specific process for an individual accessory subunit. Reason: Complex I is the entry point of the OXPHOS/respiratory chain, so aerobic respiration is a correct but broad process. Kept as non-core; the specific core process is the NADH-> ubiquinone electron transport (GO:0006120). Supporting Evidence: PMID:30030361 it is now well established that complexes I, III and IV interact with each other, forming the so-called respiratory supercomplexes |
| GO:0042776 proton motive force-driven mitochondrial ATP synthesis | NAS PMID:30030361 Assembly of mammalian oxidative phosphorylation complexes I-... | MARK AS OVER ANNOTATED | Summary: Author-stated (NAS, ComplexPortal) involvement in proton motive force-driven ATP synthesis. ATP synthesis is carried out by Complex V (ATP synthase); Complex I only contributes to the proton-motive force. This over-reaches for a matrix-side accessory subunit of Complex I. Reason: GO:0042776 describes the chemiosmotic ATP synthesis step performed by ATP synthase. NDUFS6, an accessory subunit of Complex I, does not perform or directly enable ATP synthesis; Complex I's contribution is generating the proton gradient. The term is over-annotated for this subunit. Supporting Evidence: PMID:30030361 The human enzymes comprise core proteins, performing the catalytic activities, and a large number of 'supernumerary' subunits that play essential roles in assembly, regulation and stability. |
| GO:0045271 respiratory chain complex I | IPI PMID:28844695 Architecture of Human Mitochondrial Respiratory Megacomplex ... | ACCEPT | Summary: Physical-interaction (IPI, ComplexPortal) evidence placing NDUFS6 in respiratory chain complex I, from the cryo-EM megacomplex study. Confirms complex membership. Reason: Direct structural/interaction evidence of Complex I membership; fully consistent with the other complex membership annotations. Supporting Evidence: PMID:28844695 reveals the precise assignment of individual subunits of human CI and CIII |
| GO:0005739 mitochondrion | HTP PMID:34800366 Quantitative high-confidence human mitochondrial proteome an... | KEEP AS NON CORE | Summary: High-throughput proteomics (HTP) localisation to the mitochondrion from a quantitative high-confidence human mitochondrial proteome study. Correct but non-specific relative to the inner-membrane annotation. Reason: Confirms mitochondrial localisation but is a broad parent term; the more informative inner membrane annotation is retained as the primary location. Not wrong, so kept as non-core. Supporting Evidence: file:human/NDUFS6/NDUFS6-uniprot.txt Mitochondrion inner membrane |
| GO:0045271 respiratory chain complex I | IDA PMID:12611891 The subunit composition of the human NADH dehydrogenase obta... | ACCEPT | Summary: Direct (IDA, UniProtKB) evidence of Complex I membership from one-step immunopurification and mass-spectrometric identification of the human NADH dehydrogenase subunits, which identified NDUFS6 as a component (IP fraction). Reason: NDUFS6 was directly identified as a subunit of immunopurified human Complex I by mass spectrometry. Strong experimental support for complex membership. Supporting Evidence: PMID:12611891 we can resolve and identify the human homologues of 42 polypeptides detected so far in the more extensively studied beef heart complex I |
| GO:0045271 respiratory chain complex I | NAS PMID:15372108 NDUFS6 mutations are a novel cause of lethal neonatal mitoch... | ACCEPT | Summary: Author-stated (NAS) Complex I membership from the study identifying NDUFS6 mutations as a cause of complex I deficiency. Consistent with all other membership evidence. Reason: NDUFS6 is described as a complex I subunit gene, and its loss causes assembly-defective Complex I deficiency, confirming membership. Supporting Evidence: PMID:15372108 NDUFS6, a complex I subunit gene not previously associated with complex I deficiency |
| GO:0045271 respiratory chain complex I | IDA PMID:27626371 Accessory subunits are integral for assembly and function of... | ACCEPT | Summary: Direct (IDA, UniProtKB) evidence of Complex I membership from the systematic accessory-subunit knockout/quantitative-proteomics study, which characterised NDUFS6 among the accessory subunits integral to Complex I. Reason: This study (gene editing of every accessory subunit) establishes NDUFS6 as an integral accessory subunit of human Complex I. Strong experimental support. Supporting Evidence: PMID:27626371 Accessory subunits are integral for assembly and function of human mitochondrial complex I |
| GO:0045271 respiratory chain complex I | NAS PMID:9878551 cDNA of eight nuclear encoded subunits of NADH:ubiquinone ox... | ACCEPT | Summary: Author-stated (NAS) Complex I membership from the early cDNA characterisation of the nuclear-encoded Complex I subunits. Consistent with all other membership evidence. Reason: Part of the foundational characterisation of the human Complex I subunit set; membership is corroborated by later experimental studies. Supporting Evidence: PMID:9878551 NADH:ubiquinone oxidoreductase (complex I) is an extremely complicated multiprotein complex located in the inner mitochondrial membrane |
| GO:0005743 mitochondrial inner membrane | TAS Reactome:R-HSA-163217 | ACCEPT | Summary: Traceable-author (TAS, Reactome) localisation to the mitochondrial inner membrane, from the Reactome reaction in which Complex I oxidises NADH and reduces CoQ. Correct location. Reason: Reactome curates Complex I (and hence NDUFS6) at the mitochondrial inner membrane, consistent with the UniProt location and direct evidence. Supporting Evidence: file:human/NDUFS6/NDUFS6-uniprot.txt Mitochondrion inner membrane |
| GO:0005743 mitochondrial inner membrane | TAS Reactome:R-HSA-6799179 | ACCEPT | Summary: Traceable-author (TAS, Reactome) localisation to the mitochondrial inner membrane, from a Complex I assembly reaction (peripheral arm subunits binding the 815 kDa intermediate). Correct location. Reason: Reactome assembly reactions place NDUFS6 within the inner-membrane-associated Complex I holoenzyme. Consistent with all other localisation evidence. Supporting Evidence: file:human/NDUFS6/NDUFS6-uniprot.txt Mitochondrion inner membrane |
| GO:0005743 mitochondrial inner membrane | TAS Reactome:R-HSA-6799196 | ACCEPT | Summary: Traceable-author (TAS, Reactome) localisation to the mitochondrial inner membrane, from the final Complex I biogenesis reaction (dissociation of assembly factors yielding mature Complex I). Correct location. Reason: Reactome curates mature Complex I (including NDUFS6) at the mitochondrial inner membrane. Consistent with the curated UniProt location. Supporting Evidence: file:human/NDUFS6/NDUFS6-uniprot.txt Mitochondrion inner membrane |
| GO:0005743 mitochondrial inner membrane | TAS Reactome:R-HSA-6800870 | ACCEPT | Summary: Traceable-author (TAS, Reactome) localisation to the mitochondrial inner membrane, from the reaction in which NDUF subunits assemble into the FP subcomplex. Correct location. Reason: Reactome places NDUFS6 in the inner-membrane-associated Complex I assembly, consistent with all other localisation evidence. Supporting Evidence: file:human/NDUFS6/NDUFS6-uniprot.txt Mitochondrion inner membrane |
| GO:0006120 mitochondrial electron transport, NADH to ubiquinone | NAS PMID:9878551 cDNA of eight nuclear encoded subunits of NADH:ubiquinone ox... | ACCEPT | Summary: Author-stated (NAS) involvement in mitochondrial electron transport from NADH to ubiquinone, from the cDNA characterisation paper. This is the core process of the complex NDUFS6 belongs to. Reason: Correct core process; the paper explicitly describes NADH->ubiquinone electron transport as the main function of Complex I, of which NDUFS6 is a subunit. Supporting Evidence: PMID:9878551 Its main function is the transport of electrons from NADH to ubiquinone |
| GO:0008137 NADH dehydrogenase (ubiquinone) activity | NAS PMID:9878551 cDNA of eight nuclear encoded subunits of NADH:ubiquinone ox... | MARK AS OVER ANNOTATED | Summary: Author-stated (NAS) enables NADH dehydrogenase (ubiquinone) activity. This is the catalytic activity of the Complex I holoenzyme, not of NDUFS6 individually: NDUFS6 is an accessory subunit that is believed not to be involved in catalysis and carries no electron-transfer Fe-S cluster. Reason: The NADH:ubiquinone oxidoreductase activity is a property of the assembled complex (its core catalytic and redox-cofactor-bearing subunits), not of this non-catalytic accessory subunit. NDUFS6 contributes to the activity by supporting assembly/stability of the N-module, but does not independently enable it. Retained at the complex level via contributes_to in core_functions rather than as a subunit enables annotation. Supporting Evidence: file:human/NDUFS6/NDUFS6-uniprot.txt Accessory subunit of the mitochondrial membrane respiratory |
| GO:0006120 mitochondrial electron transport, NADH to ubiquinone | NAS PMID:9647766 cDNA sequence and chromosomal localization of the remaining ... | ACCEPT | Summary: Author-stated (NAS) involvement in NADH-to-ubiquinone electron transport, from the cDNA cloning paper that first described NDUFS6 as an IP-fraction subunit of Complex I. Core process of the complex. Reason: Correct core process for the complex NDUFS6 is part of; duplicates the well-supported GO:0006120 involvement. Supporting Evidence: PMID:9647766 NADH:ubiquinone oxidoreductase (complex I) of the mitochondrial respiratory |
| GO:0008137 NADH dehydrogenase (ubiquinone) activity | NAS PMID:9647766 cDNA sequence and chromosomal localization of the remaining ... | MARK AS OVER ANNOTATED | Summary: Author-stated (NAS) enables NADH dehydrogenase (ubiquinone) activity. As above, this is the catalytic activity of the Complex I holoenzyme, not of the non-catalytic NDUFS6 accessory subunit. Reason: NDUFS6 is believed not to be involved in catalysis and does not carry a redox cofactor; the enzymatic NADH dehydrogenase activity belongs to the assembled complex. Best captured as a contributes_to relationship at the complex level (see core_functions). Supporting Evidence: file:human/NDUFS6/NDUFS6-uniprot.txt Accessory subunit of the mitochondrial membrane respiratory |
| GO:0009055 electron transfer activity | NAS PMID:9647766 cDNA sequence and chromosomal localization of the remaining ... | MARK AS OVER ANNOTATED | Summary: Author-stated (NAS) enables electron transfer activity. Electron transfer within Complex I is carried out by the FMN and Fe-S cluster-bearing catalytic core subunits (e.g. NDUFV1/NDUFS1). NDUFS6 carries no electron-transfer cofactor of the redox wire. Reason: Despite the "iron-sulfur protein" name, NDUFS6 is a non-catalytic accessory subunit with a structural CHCC zinc motif, not an Fe-S redox-wire subunit; it does not itself carry electron transfer activity. The activity resides in the cofactor-bearing core subunits of the complex. Supporting Evidence: file:human/NDUFS6/NDUFS6-uniprot.txt Accessory subunit of the mitochondrial membrane respiratory |
| GO:0032981 mitochondrial respiratory chain complex I assembly | IMP PMID:27626371 Accessory subunits are integral for assembly and function of... | NEW | Summary: Proposed new annotation capturing the specific role of NDUFS6 established experimentally: it is an accessory subunit required for assembly and stability of Complex I. Systematic gene-editing knockouts of accessory subunits showed that most are strictly required for assembly of a functional complex and that loss of a subunit destabilises the others in its structural module. Reason: The strongest, most specific functional characterisation of NDUFS6 is its requirement for Complex I assembly/stability (N-module), yet GOA lacks GO:0032981. Adding it captures the accessory subunit's real biological role, complementing the catalytic complex-level terms. Supported by IMP-quality gene-editing/proteomics evidence (PMID:27626371) and the disease genetics (assembly-defective Complex I in NDUFS6 patients, PMID:15372108). Supporting Evidence: PMID:27626371 we use gene editing to generate human knockout cell lines for each accessory subunit. We show that 25 subunits are strictly required for assembly of a functional complex PMID:15372108 all but 1 of which showed abnormalities of complex I assembly |
| GO:0005198 structural molecule activity | IMP PMID:27626371 Accessory subunits are integral for assembly and function of... | NEW | Summary: Proposed new subunit-specific molecular function. NDUFS6 is a non-catalytic accessory subunit whose role in Complex I is structural: it stabilises the N-module of the peripheral arm and is required for assembly of a functional holoenzyme. Structural molecule activity is the appropriate subunit-level MF, in place of the (over-annotated) complex-level catalytic terms. Reason: NDUFS6 is believed not to be involved in catalysis; its contribution to Complex I is as a structural constituent that stabilises the N-module during assembly (PMID:27626371). GO:0005198 captures this subunit-specific function that the enables GO:0008137/GO:0009055 catalytic terms mis-assign to the individual subunit. This underpins the core_functions molecular_function. Supporting Evidence: PMID:27626371 Analysis of proteomic changes after the loss of specific modules file:human/NDUFS6/NDUFS6-uniprot.txt Accessory subunit of the mitochondrial membrane respiratory |
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Download this section (compressed HTML)Q: Does the CHCC zinc-binding motif of NDUFS6 coordinate a structural zinc ion, and is this metal coordination required for N-module assembly/stability rather than for any redox chemistry?
Experiment: Structure-guided mutagenesis of the NDUFS6 CHCC (zf-CHCC) cysteines/histidines followed by quantitative Complex I assembly and activity assays (BN-PAGE, complexome profiling) in NDUFS6 knockout cells reconstituted with wild-type vs motif-mutant NDUFS6, to test whether zinc coordination is required for N-module stabilisation.
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