Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Global conformations of complex I are distinguished by the binding of a unique interdomain bridging subunit.
Journal, issue, pages	Sci Adv, Vol. 11, Issue 40, Page eadz0693, Year 2025
Publish date	Oct 3, 2025
Authors	Chris Seunggyu Lee / Daniel N Grba / John J Wright / Bozhidar S Ivanov / Judy Hirst /
PubMed Abstract	Complex I (CI; NADH ubiquinone oxidoreductase) is central to energy generation and metabolic homeostasis in mammalian cells but contributes to adverse outcome pathways under challenging conditions. ...Complex I (CI; NADH ubiquinone oxidoreductase) is central to energy generation and metabolic homeostasis in mammalian cells but contributes to adverse outcome pathways under challenging conditions. During ischemia, mammalian CI transitions from a turnover-ready, structurally "closed" state toward a dormant "open" state that prevents it from functioning in reverse during reperfusion to produce reactive oxygen species. Unfortunately, simpler, genetically tractable CI models do not recapitulate the same regulatory behavior, compromising mechanistic studies. Here, we report the structure of isolated CI from the yeast (-CI) and identify distinct closed and open states that resemble those of mammalian CI. Notably, a hitherto-unknown protein (NUQM) completes an interdomain bridge in only the closed state, implying that NUQM stabilizes it by restricting the conformational changes of opening. The direct correlation of NUQM binding with closed/open status in -CI provides opportunities for investigating regulatory mechanisms relevant to reversible catalysis and ischemia-reperfusion injury.
External links	Sci Adv / PubMed:41032597 / PubMed Central
Methods	EM (single particle)
Resolution	2.8 - 20.0 Å
Structure data	52875 9iho EMDB-52875, PDB-9iho: Open state without NUQM and without flavoprotein (classification state 4) of Pichia pastoris mitochondrial complex I in cMSP26 nanodiscs Method: EM (single particle) / Resolution: 3.8 Å 52876 9ihp EMDB-52876, PDB-9ihp: Open state without NUQM and with flavoprotein (classification state 3) of Pichia pastoris mitochondrial complex I in cMSP26 nanodiscs Method: EM (single particle) / Resolution: 3.34 Å 52877 9ihq EMDB-52877, PDB-9ihq: Closed state with NUQM and without flavoprotein (classification state 2) of Pichia pastoris mitochondrial complex I in cMSP26 nanodiscs Method: EM (single particle) / Resolution: 2.9 Å 52878 9ihr EMDB-52878, PDB-9ihr: Closed state with NUQM and with flavoprotein (classification state 1) of Pichia pastoris mitochondrial complex I in cMSP26 nanodiscs Method: EM (single particle) / Resolution: 2.8 Å EMDB-52890: NUQM-free state of Pichia pastoris mitochondrial complex I reconstituted into proteoliposomes Method: EM (single particle) / Resolution: 8.2 Å EMDB-52891: NUQM-bound state of Pichia pastoris mitochondrial complex I reconstituted into proteoliposomes Method: EM (single particle) / Resolution: 4.7 Å EMDB-52892: Flavoprotein (NUHM and NUBM)-free state of Pichia pastoris mitochondrial complex I reconstituted into proteoliposomes Method: EM (single particle) / Resolution: 20.0 Å EMDB-52893: Flavoprotein (NUHM and NUBM)-containing state of Pichia pastoris mitochondrial complex I reconstituted into proteoliposomes Method: EM (single particle) / Resolution: 4.7 Å
Chemicals	ChemComp-SF4: IRON/SULFUR CLUSTER ChemComp-PLC: DIUNDECYL PHOSPHATIDYL CHOLINE / phospholipidYM ChemComp-K: Unknown entry ChemComp-3PE: 1,2-Distearoyl-sn-glycerophosphoethanolamine / phospholipidYM ChemComp-CDL: CARDIOLIPIN / phospholipidYM ChemComp-NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE ChemComp-ZN: Unknown entry ChemComp-EHZ: ~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] (3~{S})-3-oxidanyltetradecanethioate ChemComp-FES: FE2/S2 (INORGANIC) CLUSTER ChemComp-FMN*: FLAVIN MONONUCLEOTIDE
Source	komagataella pastoris (fungus) Komagataella phaffii (fungus)
Keywords	MEMBRANE PROTEIN / NADH:ubiquinone oxidoreductase nanodisc membrane protein complex