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Open data
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Basic information
| Entry | Database: PDB / ID: 9q8i | |||||||||||||||||||||
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| Title | Cryo-EM structure of E. coli complex I variant V96P/N142M (NuoE) | |||||||||||||||||||||
Components | (NADH-quinone oxidoreductase subunit ...) x 13 | |||||||||||||||||||||
Keywords | MEMBRANE PROTEIN / Respiratory chain / Complex I / NADH ubiquinone oxidoreductase / electron transport / proton transport | |||||||||||||||||||||
| Function / homology | Function and homology informationTranslocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH dehydrogenase (quinone) (non-electrogenic) activity / NADH dehydrogenase complex / cellular respiration / molybdopterin cofactor binding / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / ubiquinone binding / electron transport coupled proton transport / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity ...Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / NADH dehydrogenase (quinone) (non-electrogenic) activity / NADH dehydrogenase complex / cellular respiration / molybdopterin cofactor binding / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / ubiquinone binding / electron transport coupled proton transport / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / proton transmembrane transport / aerobic respiration / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / iron ion binding / metal ion binding / membrane / plasma membrane / cytoplasm Similarity search - Function | |||||||||||||||||||||
| Biological species | ![]() | |||||||||||||||||||||
| Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.35 Å | |||||||||||||||||||||
Authors | Seifermann, T. / Wohlwend, D. / Friedrich, T. | |||||||||||||||||||||
| Funding support | Germany, 2items
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Citation | Journal: Structure / Year: 2026Title: Structural changes shifting the redox potential of the outlying cluster N1a in respiratory complex I. Authors: Daniel Wohlwend / Thilo Seifermann / Emmanuel Gnandt / Marta Vranas / Stefan Gerhardt / Thorsten Friedrich / ![]() Abstract: Energy-converting NADH:ubiquinone oxidoreductase, respiratory complex I, is central to energy metabolism by coupling NADH oxidation and quinone reduction with proton translocation across the membrane. ...Energy-converting NADH:ubiquinone oxidoreductase, respiratory complex I, is central to energy metabolism by coupling NADH oxidation and quinone reduction with proton translocation across the membrane. Electrons are transferred from the primary acceptor flavin mononucleotide via a chain of iron-sulfur clusters to quinone. The enigmatic cluster N1a is conserved, but not part of this electron transfer chain. We reported on variants of the complex in which N1a is not detectable by EPR spectroscopy. This was tentatively attributed to the lower redox potential of the variant N1a. However, it remained an open question, whether the variants contain this cluster at all. Here, we determined the structures of these variants by X-ray crystallography and cryogenic-electron microscopy. Cluster N1a is present in all variants and the shift of its redox potential is explained by nearby structural changes. A role of the cluster for the mechanism of the complex is discussed. | |||||||||||||||||||||
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 9q8i.cif.gz | 945.5 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb9q8i.ent.gz | 757.2 KB | Display | PDB format |
| PDBx/mmJSON format | 9q8i.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q8/9q8i ftp://data.pdbj.org/pub/pdb/validation_reports/q8/9q8i | HTTPS FTP |
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-Related structure data
| Related structure data | ![]() 52895MC ![]() 9he5C ![]() 9hegC ![]() 9hemC ![]() 9henC M: map data used to model this data C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
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Assembly
| Deposited unit | ![]()
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Components
-NADH-quinone oxidoreductase subunit ... , 13 types, 13 molecules ABCEFGHIJKLMN
| #1: Protein | Mass: 16474.283 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: P0AFC3, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
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| #2: Protein | Mass: 25081.809 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: P0AFC7, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
| #3: Protein | Mass: 68321.945 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: P33599, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
| #4: Protein | Mass: 18629.125 Da / Num. of mol.: 1 / Mutation: V96P, N142M Source method: isolated from a genetically manipulated source Details: Point mutations V96P and N142M have been introduced by means of site-directed mutagenesis Source: (gene. exp.) ![]() ![]() References: UniProt: P0AFD1, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
| #5: Protein | Mass: 51208.352 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The sequence MRGSHHHHHHTDPALRA was added in cloning and is an affinity sequence used for immobilized metal ion affinity chromatography, followed by an eight-amino-acid linker preceding the N-terminus of NuoF. Source: (gene. exp.) ![]() ![]() References: UniProt: P31979, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
| #6: Protein | Mass: 100419.211 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: P33602, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
| #7: Protein | Mass: 36240.922 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: P0AFD4, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
| #8: Protein | Mass: 20562.771 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: P0AFD6, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
| #9: Protein | Mass: 19889.551 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: P0AFE0, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
| #10: Protein | Mass: 10852.961 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: P0AFE4, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
| #11: Protein | Mass: 66483.609 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: P33607, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
| #12: Protein | Mass: 56560.090 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: P0AFE8, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
| #13: Protein | Mass: 52072.672 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: P0AFF0, Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions |
-Non-polymers , 7 types, 139 molecules 












| #14: Chemical | ChemComp-3PE / #15: Chemical | ChemComp-SF4 / #16: Chemical | #17: Chemical | ChemComp-FMN / | #18: Chemical | ChemComp-CA / | #19: Chemical | #20: Water | ChemComp-HOH / | |
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-Details
| Has ligand of interest | Y |
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| Has protein modification | N |
-Experimental details
-Experiment
| Experiment | Method: ELECTRON MICROSCOPY |
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| EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
| Component | Name: Respiratory complex I / Type: COMPLEX / Entity ID: #1-#13 / Source: RECOMBINANT | ||||||||||||||||||||||||||||||
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| Molecular weight | Value: 0.542 MDa / Experimental value: NO | ||||||||||||||||||||||||||||||
| Source (natural) | Organism: ![]() | ||||||||||||||||||||||||||||||
| Source (recombinant) | Organism: ![]() | ||||||||||||||||||||||||||||||
| Buffer solution | pH: 6 | ||||||||||||||||||||||||||||||
| Buffer component |
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| Specimen | Conc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
| Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||||||||||||
| Vitrification | Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 277 K / Details: BLOTTING TIME FOR 6 S WITH FILTER PAPER |
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Electron microscopy imaging
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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| Microscopy | Model: TFS KRIOS |
| Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
| Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 500 nm |
| Image recording | Electron dose: 40 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k) |
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Processing
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| Image processing |
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| CTF correction |
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| 3D reconstruction | Details: THE COMPOSITE MAP WAS CREATED IN UCSF CHIMERAX USING THREE FOCUSED MAPS AND THE CONSENSUS MAP. / Entry-ID: 9Q8I / Num. of particles: 95103 / Resolution: 2.35 Å / Resolution method: FSC 0.143 CUT-OFF / Symmetry type: POINT
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| Refinement | Highest resolution: 2.35 Å |
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Germany, 2items
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FIELD EMISSION GUN