Affinage

NDUFS3

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

Length
264 aa
Mass
30.2 kDa
Annotated
2026-06-10
25 papers in source corpus 12 papers cited in narrative 12 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 6/6 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

NDUFS3 is a non-catalytic core subunit of mitochondrial respiratory Complex I (CI) that is required for the stepwise, modular assembly of the enzyme (PMID:17209039, PMID:33882309). During biogenesis, NDUFS3 enters early ~100–150 kDa assembly intermediates that subsequently incorporate mitochondrially encoded subunits, defining the entry point of mtDNA-encoded subunits into CI (PMID:17209039). Loss of NDUFS3 drives hierarchical, modular CI disassembly in which the ND4 module remains stable and bound to the assembly factor TMEM126A, while complete ablation still permits assembly of a small amount of functional CI (PMID:33882309). The supply of functional NDUFS3 is regulated upstream by SRSF1, which binds exon 6 of Ndufs3 pre-mRNA to promote its inclusion and ensure proper splicing (PMID:38569495), and the protein is stabilized through physical interaction with DJ-1/PARK7, an interaction weakened by oxidative stress (PMID:29849492). Beyond its bioenergetic role, NDUFS3-dependent OXPHOS output is coupled to metabolic reprogramming: its loss reduces CI activity and shifts cells toward aerobic glycolysis in a ROS-dependent manner (PMID:23519235), whereas elevated NDUFS3 enhances OXPHOS and purine nucleotide biosynthesis through an AMPK–PRPS1 signaling axis to support proliferation (PMID:40404919). Pathogenic NDUFS3 mutations decrease protein levels and CI assembly, causing Complex I deficiency and late-onset Leigh syndrome with optic atrophy (PMID:14729820, PMID:30140060).

Mechanistic history

Synthesis pass · year-by-year structured walk · 12 steps
  1. 2004 Medium

    Establishing whether NDUFS3 is merely associated with CI or an essential structural component answered the question of its functional necessity and clinical relevance.

    Evidence Sequencing of NDUFS3 in CI-deficient patients with biochemical confirmation in cultured amniocytes

    PMID:14729820

    Open questions at the time
    • Does not resolve at which assembly step NDUFS3 acts
    • Mechanism linking mutation to loss of activity not defined
  2. 2007 High

    Defining when and how NDUFS3 enters CI clarified the order of modular assembly and pinpointed the entry of mtDNA-encoded subunits.

    Evidence Inducible NDUFS3-GFP in HEK293 cells with blue native Western blot and mitochondrial translation inhibition

    PMID:17209039

    Open questions at the time
    • Identity of all subcomplex partners not fully resolved
    • Assembly factors recruiting NDUFS3 not identified at this stage
  3. 2013 Medium

    Determining the consequences of NDUFS3 loss for cellular metabolism showed it couples CI output to the choice between OXPHOS and glycolysis via ROS.

    Evidence Stable shRNA knockdown in HEK293 cells with Seahorse flux, ROS measurement, and CI activity assays

    PMID:23519235

    Open questions at the time
    • Molecular link between ROS and glycolytic switch not defined
    • Single cell type
  4. 2013 Medium

    Characterizing how disease mutations alter NDUFS3 itself provided a structural basis for assembly failure.

    Evidence Recombinant wild-type and double-mutant (T145I+R199W) NDUFS3 analyzed by fluorescence, CD, and aggregation assays

    PMID:24028823

    Open questions at the time
    • In vitro behavior not validated in mitochondria
    • Aggregation propensity not linked to specific assembly intermediate defect
  5. 2018 Medium

    Identifying DJ-1/PARK7 as a physical partner addressed how NDUFS3 stability is protected under oxidative conditions.

    Evidence Co-immunoprecipitation and Western blot with CI activity assay in a rat asthenozoospermia model

    PMID:29849492

    Open questions at the time
    • Direct vs. indirect interaction not resolved
    • Mechanism by which DJ-1 stabilizes NDUFS3 unknown
    • Single model system
  6. 2018 Medium

    Patient-derived compound heterozygous mutations confirmed that NDUFS3 levels directly limit CI assembly, reinforcing its causal role in disease.

    Evidence MitoExome sequencing with BN-PAGE and Western blot in patient lymphoblastoid cells

    PMID:30140060

    Open questions at the time
    • Genotype–phenotype correlation across mutations not established
    • Tissue-specific severity not addressed
  7. 2021 High

    Graded NDUFS3 depletion resolved the hierarchy of CI disassembly and revealed TMEM126A as an ND4-module assembly factor.

    Evidence Knockout and knockdown in multiple cell lines with functional CI assays, BN-PAGE, and TMEM126A co-IP

    PMID:33882309

    Open questions at the time
    • How residual CI assembles without NDUFS3 unexplained
    • Structural detail of TMEM126A–ND4 module interaction not defined
  8. 2022 Medium

    Using NDUFS3-null cells as a CI-null tool distinguished true CI-targeting drugs from CI-independent agents.

    Evidence NDUFS3 knockout cancer cell lines with antiproliferative assays and molecular docking into the quinone pocket

    PMID:36349591

    Open questions at the time
    • Docking predictions not confirmed by structural binding data
    • NDUFS3's own role in the quinone pocket not addressed
  9. 2024 Medium

    Identifying SRSF1-mediated splicing of Ndufs3 exon 6 defined an upstream control point governing functional NDUFS3 production and tissue energetics.

    Evidence Adipocyte-specific SRSF1 knockout mice with snRNA-seq, binding assays, TEM, and CI activity measurement

    PMID:38569495

    Open questions at the time
    • Whether splicing regulation operates in other tissues unknown
    • Other SRSF1 targets contributing to phenotype not excluded
  10. 2024 Low

    Testing NDUFS3 reduction in a PINK1 Parkinson's model probed whether lowering CI activity can be protective via reduced oxidative stress.

    Evidence NDUFS3 RNAi in PINK1B9 Drosophila with behavioral, viability, and ROS phenotyping

    PMID:39102941

    Open questions at the time
    • Single genetic manipulation with limited mechanistic depth
    • Not confirmed in mammalian neurons
    • Direct ROS-protection causality not established
  11. 2025 Medium

    Linking NDUFS3 loss to RAB7 and the endolysosomal pathway revealed mitochondria–lysosome crosstalk influencing tumor invasiveness.

    Evidence RNAi silencing in pancreatic cancer cells with Seahorse, TEM, invasion assays, and Western blot

    PMID:40369571

    Open questions at the time
    • Signal connecting mitochondrial dysfunction to RAB7 downregulation undefined
    • Single cancer type
  12. 2025 Medium

    Defining the NDUFS3–AMPK–PRPS1 axis explained how NDUFS3-driven OXPHOS output is converted into purine biosynthesis and proliferative advantage.

    Evidence NDUFS3 overexpression and knockdown in melanoma cells with Seahorse, AMPK phosphorylation, and PRPS1 activity assays

    PMID:40404919

    Open questions at the time
    • Generalizability beyond melanoma not established
    • Direct vs. ATP-mediated regulation of AMPK by NDUFS3 not dissected

Open questions

Synthesis pass · forward-looking unresolved questions
  • How NDUFS3 abundance and assembly state are integrated across regulatory inputs (SRSF1 splicing, DJ-1 stabilization, ROS) to control CI biogenesis and downstream metabolic signaling in a tissue-specific manner remains unresolved.
  • No unified model connecting upstream regulators to assembly intermediates
  • Structural mechanism of NDUFS3 within early intermediates undefined
  • Tissue-specific phenotypic determinants unknown

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0005198 structural molecule activity 3
Localization
GO:0005739 mitochondrion 3
Pathway
R-HSA-1430728 Metabolism 2 R-HSA-1852241 Organelle biogenesis and maintenance 2
Partners
PARK7SRSF1TMEM126A
Complex memberships
Complex I ND4 moduleMitochondrial respiratory Complex I

Evidence

Reading pass · 12 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2007 NDUFS3 is incorporated into Complex I through stepwise assembly: using an inducible NDUFS3-GFP expression system, six distinct NDUFS3-GFP-containing subcomplexes were identified on blue native Western blots, and inhibition of mitochondrial translation caused accumulation of ~100 and ~150 kDa NDUFS3-containing subcomplexes, demonstrating these are true assembly intermediates. Incorporation of at least one mitochondrially-encoded subunit was shown to occur at this step, defining the entry point of mitochondrial DNA-encoded subunits into Complex I assembly. Inducible NDUFS3-GFP expression in HEK293 cells, blue native Western blot, differential detergent solubilization, heat incubation, mitochondrial translation inhibition The Journal of biological chemistry High 17209039
2021 NDUFS3 is a non-catalytic core subunit of Complex I whose complete ablation in diverse mammalian cell types still permits a small amount of functional CI to be assembled. Gradual reduction of NDUFS3 causes hierarchical, modular disassembly in which the ND4 module remains stable and bound to TMEM126A, thereby revealing TMEM126A as a CI assembly factor that interacts with the ND4-module intermediate. NDUFS3 knockout and knockdown in multiple mammalian cell lines, functional CI assays, blue native PAGE, co-immunoprecipitation of TMEM126A with ND4-module Cell reports High 33882309
2004 Mutations in NDUFS3 (the seventh core subunit of Complex I, encoding an Fe-S protein) cause Complex I deficiency and late-onset Leigh syndrome with optic atrophy, establishing NDUFS3 as an essential structural component of the Complex I catalytic core whose loss abolishes enzyme activity. DHPLC and sequencing of NDUFS3 in Complex I-deficient patients; biochemical diagnosis of CI deficiency in cultured amniocytes confirmed by mutation identification Journal of medical genetics Medium 14729820
2013 NDUFS3 gene silencing in human embryonic kidney cells causes mitochondrial dysfunction, reduces Complex I activity, and induces a switch to aerobic glycolysis in a manner dependent on NDUFS3 protein levels; sustained free radical imbalance (ROS) is required to maintain the glycolytic metabolic switch in cells with the most severe NDUFS3 suppression. Stable lentiviral shRNA knockdown of NDUFS3 in HEK293 cells, Seahorse metabolic flux analysis, ROS measurement, Complex I activity assays Biology open Medium 23519235
2013 The disease-associated double mutant (T145I + R199W) NDUFS3 protein exhibits altered secondary and tertiary structure, altered polarity around tryptophan residues, and a higher tendency toward aggregation compared to wild-type protein, providing a structural basis for how these mutations disrupt Complex I assembly. Recombinant expression and purification of wild-type and double-mutant NDUFS3 in E. coli, steady-state and time-resolved fluorescence spectroscopy, CD spectroscopy, Thioflavin-T and Congo red dye binding, thermal and Gdn-HCl denaturation Biochimie Medium 24028823
2018 DJ-1 (PARK7 gene product) physically interacts with NDUFS3 in rat testes; this interaction is weakened by oxidative stress (ornithine treatment), and reduced DJ-1 is accompanied by decreased NDUFS3 expression and reduced Complex I activity, suggesting DJ-1 protects NDUFS3 stability/function. Co-immunoprecipitation of DJ-1 and NDUFS3 in rat testes, Western blot of NDUFS3 and DJ-1, Complex I activity assay in rat asthenozoospermia model Mediators of inflammation Medium 29849492
2018 Two compound heterozygous missense mutations in NDUFS3 (c.418 C>T/p.R140W and c.595 C>T/p.R199W) decrease both NDUFS3 protein levels and Complex I assembly in patient-derived lymphoblastoid cells, confirming that NDUFS3 is required for proper Complex I assembly. Next-generation sequencing (MitoExome), Western blot and blue native PAGE of Complex I in patient lymphoblastoid cells vs. controls Journal of human genetics Medium 30140060
2024 The splicing factor SRSF1 binds constitutive exon 6 of Ndufs3 pre-mRNA and promotes its inclusion; adipocyte-specific SRSF1 deficiency causes impaired Ndufs3 splicing, reduced functional NDUFS3 protein, defective Complex I assembly and activity, fragmented/degenerated mitochondria, and impaired thermogenesis in brown adipose tissue. SRSF1 conditional knockout in adipocytes (mice), single-nucleus RNA sequencing, transmission electron microscopy, RIP or CLIP-based binding assay of SRSF1 to Ndufs3 exon 6, Complex I activity assay Advanced science Medium 38569495
2022 NDUFS3 knockout cancer cells showed that BAY 87-2243 and EVP 4593 are selective Complex I inhibitors (their antiproliferative effects are abolished in CI-null cells), while metformin's antiproliferative effects are largely CI-independent. Molecular docking indicates BAY 87-2243 and EVP 4593 bind in the quinone-binding pocket of CI with amino acids conserved across species. NDUFS3 knockout cancer cell lines (CI-null model), antiproliferative assays, molecular docking into CI quinone-binding pocket Open biology Medium 36349591
2025 NDUFS3 transient silencing in pancreatic cancer cells reduces oxidative phosphorylation and causes mitochondrial morphology alterations, which leads to RAB7 downregulation and impairment of the late endocytic/lysosomal pathway, resulting in reduced invasiveness and tumorigenic potential; RAB7 modulation in turn regulates vimentin levels and mitochondrial protein levels, demonstrating bidirectional mitochondria-lysosome crosstalk downstream of NDUFS3. RNAi silencing of NDUFS3 in pancreatic cancer cells, Seahorse assay, TEM, confocal microscopy, Western blot, wound healing and FluoroBlok invasion assay, zymography Cell communication and signaling Medium 40369571
2025 In melanoma cells, elevated NDUFS3 promotes OXPHOS and the pentose phosphate pathway while attenuating glycolysis; increased ATP production inhibits AMPK, which normally phosphorylates PRPS1 to suppress its activity, so NDUFS3 overexpression leads to enhanced purine nucleotide biosynthesis and melanoma proliferation via a NDUFS3-AMPK-PRPS1 signaling axis. NDUFS3 overexpression and knockdown in melanoma cells, Seahorse metabolic flux analysis, AMPK phosphorylation assays, PRPS1 activity measurement, proliferation assays Cell death and differentiation Medium 40404919
2024 In a PINK1B9 Drosophila model of Parkinson's disease, downregulation of NDUFS3 by RNAi had a protective effect on the transgenic flies, suggesting that reducing NDUFS3-dependent Complex I activity can ameliorate PINK1 loss-of-function phenotypes via reduction of oxidative stress. NDUFS3 RNAi in MHC-Gal4/UAS PINK1B9 transgenic Drosophila, behavioral and viability phenotyping, ROS/oxidative stress measurements Neuroscience letters Low 39102941

Source papers

Stage 0 corpus · 25 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
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 24 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 22 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 NDUFS3 alleviates oxidative stress and ferroptosis in sepsis induced acute kidney injury through AMPK pathway. International immunopharmacology 16 39426231
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
2018 Downregulation of DJ-1 Fails to Protect Mitochondrial Complex I Subunit NDUFS3 in the Testes and Contributes to the Asthenozoospermia. Mediators of inflammation 14 29849492
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
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 11 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 6 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
2026 An Atypical Neurosensory-Predominant Presentation Associated with a Homozygous NDUFS3 Variant: A Diagnostic Challenge Involving Retinal and Hearing Phenotypes. Molecular syndromology 0 42232357
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

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