Affinage

NDUFS3

NADH dehydrogenase [ubiquinone] iron-sulfur protein 3, mitochondrial · UniProt O75489

Round 2 corrected
Length
264 aa
Mass
30.2 kDa
Annotated
2026-04-29
54 papers in source corpus 14 papers cited in narrative 14 extracted findings

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

NDUFS3 is a nuclear-encoded core subunit of the Q module of mitochondrial respiratory complex I that is essential for proper complex I assembly, oxidative phosphorylation, and metabolic homeostasis. It enters early assembly intermediates (~100–150 kDa subcomplexes) before mitochondrial DNA-encoded subunits are incorporated, and its gradual loss triggers hierarchical, modular complex I disassembly with the ND4 module remaining stably bound to the assembly factor TMEM126A (PMID:17209039, PMID:33882309). NDUFS3 levels control a metabolic threshold between OXPHOS and aerobic glycolysis via ROS signaling, and elevated NDUFS3-driven ATP production suppresses AMPK to relieve inhibition of PRPS1, thereby stimulating purine biosynthesis in cancer cells (PMID:23519235, PMID:40404919). Biallelic mutations in NDUFS3 cause mitochondrial complex I deficiency presenting as Leigh syndrome (PMID:14729820, PMID:30140060).

Mechanistic history

Synthesis pass · year-by-year structured walk · 9 steps
  1. 2004 High

    Identification of NDUFS3 mutations in patients with Leigh syndrome and complex I deficiency established NDUFS3 as a disease-causing core subunit of complex I, answering whether this subunit is individually essential for human bioenergetics.

    Evidence DHPLC and sequencing of NDUFS3 in complex I–deficient patients with biochemical validation in cultured amniocytes

    PMID:14729820

    Open questions at the time
    • Precise structural consequences of patient mutations on assembled complex I were unknown
    • Genotype–phenotype correlations across different NDUFS3 mutations not established
  2. 2007 High

    Tracking NDUFS3-GFP incorporation into assembly intermediates revealed that NDUFS3 enters early nucleus-encoded subcomplexes before mitochondrially-encoded subunits join, defining its temporal position in the complex I assembly pathway.

    Evidence Inducible NDUFS3-GFP in HEK293 cells with BN-PAGE, differential solubilization, and mitochondrial translation inhibition/reversal

    PMID:17209039

    Open questions at the time
    • Identity of direct binding partners within the early assembly intermediate was not resolved
    • Whether NDUFS3 acts as a scaffold or is passively incorporated remained unclear
  3. 2013 Medium

    Biophysical characterization of disease-associated NDUFS3 double mutant protein and dose-dependent knockdown studies together revealed that mutations destabilize protein structure and promote aggregation, while graded NDUFS3 loss triggers a ROS-dependent metabolic switch to aerobic glycolysis, providing both structural and metabolic mechanisms for complex I dysfunction.

    Evidence Recombinant mutant protein spectroscopy and aggregation assays; RNAi dose-response in HEK cells with metabolic profiling

    PMID:23519235 PMID:24028823

    Open questions at the time
    • Structural studies used isolated recombinant protein, not the assembled complex
    • ROS-to-glycolysis switch mechanism lacked identification of specific ROS sensor or signaling intermediates
  4. 2017 High

    Cryo-EM structure of the human respiratory megacomplex I₂III₂IV₂ resolved the precise position of NDUFS3 within the Q module, providing atomic-level context for its role in ubiquinone binding and electron transfer.

    Evidence Cryo-electron microscopy of purified human respiratory megacomplex

    PMID:28844695

    Open questions at the time
    • Dynamic conformational changes of NDUFS3 during catalysis not captured
    • Structure does not resolve assembly intermediates containing NDUFS3
  5. 2018 Medium

    DJ-1 was identified as a physical interactor that protects NDUFS3 stability, and additional Leigh syndrome mutations were biochemically validated, expanding understanding of NDUFS3 regulation and disease mechanism.

    Evidence Co-IP of DJ-1/NDUFS3 in rat testes with complex I activity assays; MitoExome sequencing with BN-PAGE in patient lymphoblastoid cells

    PMID:29849492 PMID:30140060

    Open questions at the time
    • DJ-1–NDUFS3 interaction demonstrated by single Co-IP without reciprocal validation or structural mapping
    • Whether DJ-1 acts as a chaperone or stabilizer of NDUFS3 is unresolved
  6. 2021 High

    Complete NDUFS3 ablation showed that a small amount of functional complex I can still assemble without it, overturning the assumption of absolute requirement, and revealed hierarchical modular disassembly with the ND4 module persisting bound to the newly identified assembly factor TMEM126A.

    Evidence NDUFS3 KO and KD in multiple mammalian cell types; BN-PAGE, Co-IP, quantitative proteomics, and activity assays

    PMID:33882309

    Open questions at the time
    • How a residual complex I assembles without NDUFS3 is mechanistically unexplained
    • Whether TMEM126A-ND4 module persistence has functional consequences beyond assembly stalling is unknown
  7. 2022 Medium

    NDUFS3-knockout cancer cells served as a genetic tool to demonstrate that BAY 87-2243 and EVP 4593 are selective complex I inhibitors, and molecular docking placed NDUFS3 residues within the quinone-binding pocket interaction network.

    Evidence NDUFS3 KO cell viability assays combined with molecular docking into complex I structure

    PMID:36349549

    Open questions at the time
    • Drug–NDUFS3 contacts are computational; no mutagenesis or binding data confirm direct interaction
    • Pharmacological relevance in vivo not demonstrated
  8. 2024 Medium

    Multiple studies converged to reveal upstream regulatory mechanisms and downstream signaling of NDUFS3: SRSF1 controls Ndufs3 pre-mRNA splicing required for brown adipose thermogenesis, MAZ transcriptionally upregulates NDUFS3 in melanoma, and NDUFS3 overexpression protects against sepsis-induced ferroptosis via the AMPK pathway.

    Evidence Adipocyte-specific SRSF1 KO mice with RNA binding assays and thermogenesis measurements; ChIP and reporter assays for MAZ on NDUFS3 promoter; NDUFS3 overexpression with AMPK inhibitor epistasis in sepsis-AKI models

    PMID:38569495 PMID:39426231 PMID:39532991

    Open questions at the time
    • Whether SRSF1-mediated splicing control is specific to Ndufs3 or affects other complex I subunits coordinately is unknown
    • MAZ–NDUFS3 transcriptional axis demonstrated only in melanoma
    • AMPK-dependent ferroptosis protection by NDUFS3 lacks identification of the direct AMPK-activating mechanism
  9. 2025 Medium

    NDUFS3 was placed at the center of cancer metabolic reprogramming: its loss in pancreatic cancer impairs the endolysosomal pathway via RAB7 downregulation to reduce invasiveness, while its elevation in melanoma drives a NDUFS3–AMPK–PRPS1 axis coupling OXPHOS output to purine biosynthesis.

    Evidence NDUFS3 KD in pancreatic cancer cells with Seahorse, EM, invasion assays; NDUFS3 gain/loss-of-function in melanoma with metabolic flux and PRPS1 phosphorylation analysis

    PMID:40369571 PMID:40404919

    Open questions at the time
    • RAB7 downregulation mechanism downstream of mitochondrial impairment is not defined
    • NDUFS3–AMPK–PRPS1 axis not validated in non-melanoma contexts
    • Whether NDUFS3 dosage effects on cancer metabolism reflect complex I activity versus moonlighting functions is unresolved

Open questions

Synthesis pass · forward-looking unresolved questions
  • It remains unknown whether NDUFS3 has functional roles independent of complex I, how residual complex I assembles in its complete absence, and whether the metabolic signaling axes identified in individual cancer types generalize across tissues.
  • No moonlighting function established or excluded
  • Structural basis of residual complex I assembly without NDUFS3 unresolved
  • Tissue-generalizability of NDUFS3–AMPK–PRPS1 axis untested

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0005198 structural molecule activity 3
Localization
GO:0005739 mitochondrion 4
Pathway
R-HSA-1430728 Metabolism 5 R-HSA-1643685 Disease 4
Partners
DJ-1MAZPRPS1SRSF1TMEM126A
Complex memberships
Mitochondrial complex I (NADH:ubiquinone oxidoreductase)Respiratory megacomplex I2III2IV2

Evidence

Reading pass · 14 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2004 Mutations in NDUFS3 (NADH dehydrogenase iron-sulphur protein 3), the seventh core subunit of mitochondrial complex I, were shown to cause late-onset Leigh syndrome, optic atrophy, and complex I deficiency, establishing NDUFS3 as an essential structural/functional core subunit of complex I whose loss produces severe mitochondrial disease. DHPLC and sequence analysis of NDUFS3 in complex I-deficient patients; biochemical diagnosis on cultured amniocytes Journal of medical genetics High 14729820
2007 Using an inducible NDUFS3-GFP expression system, NDUFS3 was shown to enter early, nucleus-encoded assembly intermediates (~100 and ~150 kDa subcomplexes) of mitochondrial complex I before mitochondrial DNA-encoded subunits are incorporated, defining the entry point of mitochondrially-translated subunits into the growing complex. Inducible NDUFS3-GFP expression in HEK293 cells; blue native PAGE Western blot; differential solubilization; inhibition of mitochondrial translation with reversal experiments The Journal of biological chemistry High 17209039
2013 Gene silencing of NDUFS3 in isogenic human embryonic kidney cells systematically introduced mitochondrial complex I dysfunction and triggered a metabolic switch to aerobic glycolysis (Warburg effect) in a manner dependent on NDUFS3 protein levels, with sustained free radical (ROS) imbalance required to maintain the glycolytic phenotype. RNAi-mediated gene silencing with graded NDUFS3 suppression; metabolic characterization including oxygen consumption, glycolysis, and ROS measurements in isogenic cell lines Biology open Medium 23519235
2013 The double mutant NDUFS3 protein (T145I + R199W) associated with Leigh syndrome showed altered polarity around tryptophan residues, changed fluorescence quenching parameters, altered secondary and tertiary structure, and a significantly higher tendency to aggregate compared to wild-type, as well as loss of a molten globule state at low pH, providing a structural basis for how these mutations disrupt complex I assembly. Recombinant expression and purification in E. coli; steady-state and time-resolved fluorescence spectroscopy; CD spectroscopy; Thioflavin-T and Congo red dye binding for aggregation; thermal and Gdn-HCl unfolding Biochimie Medium 24028823
2018 DJ-1 (PARK7 gene product) physically interacts with NDUFS3 in rat testes, and disruption of this interaction by ornidazole treatment reduces NDUFS3 protein levels and complex I activity, linking DJ-1's protective role against oxidative stress to maintenance of NDUFS3 integrity in sperm mitochondria. Co-immunoprecipitation of DJ-1 and NDUFS3 in rat testes; Western blot; complex I activity assay in asthenozoospermic patient sperm and rat model Mediators of inflammation Medium 29849492
2018 Two missense mutations in NDUFS3 (c.418C>T/p.R140W and c.595C>T/p.R199W) identified by next-generation sequencing in a Leigh syndrome patient caused decreased NDUFS3 protein levels and impaired complex I assembly in patient-derived lymphoblastoid cells. MitoExome next-generation sequencing; Western blot and blue native PAGE of patient lymphoblastoid cells Journal of human genetics Medium 30140060
2021 Complete ablation of NDUFS3 allows a small amount of functional complex I to still assemble in diverse mammalian cell types, demonstrating that NDUFS3 is not absolutely required for complex I biogenesis. Gradual reduction of NDUFS3 causes hierarchical, modular complex I disassembly in which the ND4 module remains stable and bound to TMEM126A (OPA7), uncovering TMEM126A as a complex I assembly factor that binds the ND4-module intermediate. NDUFS3 knockout and knockdown in multiple mammalian cell types; blue native PAGE; co-immunoprecipitation; mass spectrometry-based proteomics; functional complex I activity assays Cell reports High 33882309
2022 Using NDUFS3 knockout cancer cells devoid of complex I, BAY 87-2243 and EVP 4593 were shown to be selective complex I inhibitors whose antiproliferative effects depend on complex I, whereas metformin's antiproliferative effects were largely independent of complex I. Molecular docking indicated that BAY 87-2243 and EVP 4593 bind in the quinone-binding pocket of complex I, with NDUFS3-containing residues forming part of the interaction network. NDUFS3 knockout cell models; cell viability assays; molecular docking into complex I structure Open biology Medium 36349549
2024 The splicing factor SRSF1 binds to constitutive exon 6 of Ndufs3 pre-mRNA and promotes its inclusion; SRSF1 deficiency in mature adipocytes causes impaired Ndufs3 splicing, reduced functional NDUFS3 protein, defective mitochondrial complex I assembly and activity, mitochondrial fragmentation, and impaired thermogenic capacity of brown adipose tissue. Adipocyte-specific SRSF1 knockout mice; single-nucleus RNA sequencing; transmission electron microscopy; RNA pulldown/RIP demonstrating SRSF1 binding to Ndufs3 exon 6; complex I activity assays; thermogenesis measurements Advanced science High 38569495
2024 NDUFS3 overexpression in a sepsis-induced acute kidney injury rat model inhibited LPS-induced ferroptosis and mitochondrial damage; inhibition of AMPK by Compound C abolished this protection, placing NDUFS3 upstream of the AMPK pathway in regulating mitochondrial ROS, ferroptosis markers (MDA, GSH, iron levels), and ATP production in kidney cells. NDUFS3 overexpression in rats (hydrodynamic tail vein injection) and HK-2 cells; AMPK inhibitor (Compound C) epistasis; Western blot; MDA/GSH/iron content; Mitosox ROS; ATP assay; transmission electron microscopy International immunopharmacology Medium 39426231
2025 In pancreatic cancer cells, transient siRNA-mediated silencing of NDUFS3 caused mitochondrial deficit, reduced oxidative metabolism, and morphological mitochondrial alterations; this mitochondrial impairment led to RAB7 downregulation, impairment of the late endocytic/lysosomal pathway, and reduced cancer cell invasiveness, migration, vimentin levels, and EMT markers, linking NDUFS3-dependent mitochondrial function to mitochondria-lysosome crosstalk and cancer invasive potential. RNAi knockdown of NDUFS3 in pancreatic cancer cells; Seahorse XF assay; transmission electron microscopy; Western blot; confocal microscopy; zymography; wound healing and invasion assays; colony assays Cell communication and signaling Medium 40369571
2025 In melanoma, elevated NDUFS3 promotes oxidative phosphorylation and the pentose phosphate pathway while attenuating glycolysis; increased ATP production from NDUFS3-mediated OXPHOS suppresses AMPK activity, which in turn relieves AMPK-mediated phosphorylation/inhibition of PRPS1, thereby stimulating purine nucleotide biosynthesis and melanoma proliferation, defining a NDUFS3–AMPK–PRPS1 signaling axis. NDUFS3 overexpression and knockdown in melanoma cells; metabolic flux analysis (OXPHOS, glycolysis, PPP); AMPK activity measurement; PRPS1 phosphorylation assay; proliferation assays Cell death and differentiation Medium 40404919
2024 MAZ (Myc-associated Zinc-finger Protein) transcriptionally targets and upregulates NDUFS3 expression in melanoma, linking a transcription factor to NDUFS3-driven enhancement of mitochondrial metabolism and malignant progression. Chromatin immunoprecipitation and reporter assays demonstrating MAZ binding to NDUFS3 promoter; gain- and loss-of-function of MAZ with NDUFS3 expression readout; proliferation/migration/invasion assays Communications biology Medium 39532991
2017 Cryo-EM structure of the human respiratory megacomplex I2III2IV2 revealed the precise subunit assignment and position of NDUFS3 within the Q module of complex I in the context of the full respiratory supercomplex. Cryo-electron microscopy of human respiratory megacomplex I2III2IV2 Cell High 28844695

Source papers

Stage 0 corpus · 54 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2010 Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index. Nature genetics 2251 20935630
2012 Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. Cell 1718 22658674
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
2011 Systematic and quantitative assessment of the ubiquitin-modified proteome. Molecular cell 1334 21906983
2015 The BioPlex Network: A Systematic Exploration of the Human Interactome. Cell 1118 26186194
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
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
2011 A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles. Molecular & cellular proteomics : MCP 749 21890473
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 Genome-scale RNAi screen for host factors required for HIV replication. Cell host & microbe 627 18976975
2018 High-Density Proximity Mapping Reveals the Subcellular Organization of mRNA-Associated Granules and Bodies. Molecular cell 580 29395067
2017 Anticancer sulfonamides target splicing by inducing RBM39 degradation via recruitment to DCAF15. Science (New York, N.Y.) 533 28302793
1994 Oligo-capping: a simple method to replace the cap structure of eukaryotic mRNAs with oligoribonucleotides. Gene 492 8125298
2004 The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome research 438 15489334
2015 A Dynamic Protein Interaction Landscape of the Human Centrosome-Cilium Interface. Cell 433 26638075
2022 OpenCell: Endogenous tagging for the cartography of human cellular organization. Science (New York, N.Y.) 432 35271311
2005 Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. Genome research 409 16344560
2015 Panorama of ancient metazoan macromolecular complexes. Nature 407 26344197
2017 Architecture of Human Mitochondrial Respiratory Megacomplex I2III2IV2. Cell 391 28844695
2021 A proximity-dependent biotinylation map of a human cell. Nature 339 34079125
2007 Huntingtin interacting proteins are genetic modifiers of neurodegeneration. PLoS genetics 325 17500595
2010 Dynamics of cullin-RING ubiquitin ligase network revealed by systematic quantitative proteomics. Cell 318 21145461
2017 Genome-wide CRISPR screen identifies HNRNPL as a prostate cancer dependency regulating RNA splicing. Proceedings of the National Academy of Sciences of the United States of America 282 28611215
2010 Mass spectrometric analysis of lysine ubiquitylation reveals promiscuity at site level. Molecular & cellular proteomics : MCP 262 21139048
2021 Quantitative high-confidence human mitochondrial proteome and its dynamics in cellular context. Cell metabolism 239 34800366
2016 Mitochondrial Protein Interaction Mapping Identifies Regulators of Respiratory Chain Function. Molecular cell 220 27499296
2004 Mutant NDUFS3 subunit of mitochondrial complex I causes Leigh syndrome. Journal of medical genetics 148 14729820
2007 Identification of mitochondrial complex I assembly intermediates by tracing tagged NDUFS3 demonstrates the entry point of mitochondrial subunits. The Journal of biological chemistry 125 17209039
2013 Mitochondrial NDUFS3 regulates the ROS-mediated onset of metabolic switch in transformed cells. Biology open 39 23519235
2011 Biomarker signatures of mitochondrial NDUFS3 in invasive breast carcinoma. Biochemical and biophysical research communications 30 21867691
2021 NDUFS3 depletion permits complex I maturation and reveals TMEM126A/OPA7 as an assembly factor binding the ND4-module intermediate. Cell reports 23 33882309
2019 Metformin restores the mitochondrial membrane potentials in association with a reduction in TIMM23 and NDUFS3 in MPP+-induced neurotoxicity in SH-SY5Y cells. EXCLI journal 22 31645842
2012 Mitochondrial proteome analysis reveals depression of the Ndufs3 subunit and activity of complex I in diabetic rat brain. Journal of proteomics 21 22387129
2018 A Novel NDUFS3 mutation in a Chinese patient with severe Leigh syndrome. Journal of human genetics 20 30140060
2013 Human mitochondrial NDUFS3 protein bearing Leigh syndrome mutation is more prone to aggregation than its wild-type. Biochimie 17 24028823
2024 SRSF1 Is Required for Mitochondrial Homeostasis and Thermogenic Function in Brown Adipocytes Through its Control of Ndufs3 Splicing. Advanced science (Weinheim, Baden-Wurttemberg, Germany) 14 38569495
2024 NDUFS3 alleviates oxidative stress and ferroptosis in sepsis induced acute kidney injury through AMPK pathway. International immunopharmacology 13 39426231
2022 NDUFS3 knockout cancer cells and molecular docking reveal specificity and mode of action of anti-cancer respiratory complex I inhibitors. Open biology 13 36349549
2018 Downregulation of DJ-1 Fails to Protect Mitochondrial Complex I Subunit NDUFS3 in the Testes and Contributes to the Asthenozoospermia. Mediators of inflammation 13 29849492
2013 Reduced expression of NDUFS3 and its clinical significance in serous ovarian cancer. International journal of gynecological cancer : official journal of the International Gynecological Cancer Society 10 23446378
2023 NDUFB11 and NDUFS3 play a role in atherosclerosis and chronic stress. Aging 9 37642954
2025 NDUFS3 promotes proliferation via glucose metabolism reprogramming inducing AMPK phosphorylating PRPS1 to increase the purine nucleotide synthesis in melanoma. Cell death and differentiation 5 40404919
2021 Mitochondrial Ultrastructural Defects in NDUFS3-Related Disorder. Journal of pediatric neurosciences 5 36531773
2024 Molecular mechanisms of MAZ targeting up-regulation of NDUFS3 expression to promote malignant progression in melanoma. Communications biology 4 39532991
2023 NDUFB11 and NDUFS3 regulate arterial atherosclerosis and venous thrombosis: Potential markers of atherosclerosis and venous thrombosis. Medicine 4 37986300
2018 Correction: A novel NDUFS3 mutation in a Chinese patient with severe Leigh syndrome. Journal of human genetics 4 30266949
2025 Induced mitochondrial deficit by NDUFS3 transient silencing reduces RAB7 expression and causes lysosomal dysfunction in pancreatic cancer cells. Cell communication and signaling : CCS 3 40369571
2024 Mitochondrial dysfunction and NDUFS3: Insights from a PINK1B9 Drosophila model in Parkinson's disease pathogenesis. Neuroscience letters 3 39102941
2024 Moringa oleifera leaf extract suppresses TIMM23 and NDUFS3 expression and alleviates oxidative stress induced by Aβ1-42 in neuronal cells via activation of Akt. Research in pharmaceutical sciences 2 39006971
2025 Screening ligands interacting with NDUFS3 from Oroxylum indicum extract using bioaffinity ultrafiltration combined with in vitro protein purification. Biochemical and biophysical research communications 0 40435704