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Yorodumi- PDB-7nz1: Respiratory complex I from Escherichia coli - focused refinement ... -
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-Basic information
Entry | Database: PDB / ID: 7nz1 | ||||||
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Title | Respiratory complex I from Escherichia coli - focused refinement of cytoplasmic arm | ||||||
Components | (NADH-quinone oxidoreductase subunit ...) x 6 | ||||||
Keywords | ELECTRON TRANSPORT / NADH:ubiquinone reductase (H+-translocating) / oxidative phosphorylation | ||||||
Function / homology | Function and homology information NADH dehydrogenase complex / : / NADH:ubiquinone reductase (non-electrogenic) activity / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / molybdopterin cofactor binding / respiratory chain complex I / cellular respiration / quinone binding / ATP synthesis coupled electron transport / respiratory electron transport chain ...NADH dehydrogenase complex / : / NADH:ubiquinone reductase (non-electrogenic) activity / Translocases; Catalysing the translocation of protons; Linked to oxidoreductase reactions / molybdopterin cofactor binding / respiratory chain complex I / cellular respiration / quinone binding / ATP synthesis coupled electron transport / respiratory electron transport chain / NADH dehydrogenase (ubiquinone) activity / aerobic respiration / transmembrane transport / 2 iron, 2 sulfur cluster binding / NAD binding / FMN binding / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / iron ion binding / membrane / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli B (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.1 Å | ||||||
Authors | Kolata, P. / Efremov, R.G. | ||||||
Funding support | Belgium, 1items
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Citation | Journal: Elife / Year: 2021 Title: Structure of respiratory complex I reconstituted into lipid nanodiscs reveals an uncoupled conformation. Authors: Piotr Kolata / Rouslan G Efremov / Abstract: Respiratory complex I is a multi-subunit membrane protein complex that reversibly couples NADH oxidation and ubiquinone reduction with proton translocation against transmembrane potential. Complex I ...Respiratory complex I is a multi-subunit membrane protein complex that reversibly couples NADH oxidation and ubiquinone reduction with proton translocation against transmembrane potential. Complex I from is among the best functionally characterized complexes, but its structure remains unknown, hindering further studies to understand the enzyme coupling mechanism. Here, we describe the single particle cryo-electron microscopy (cryo-EM) structure of the entire catalytically active complex I reconstituted into lipid nanodiscs. The structure of this mesophilic bacterial complex I displays highly dynamic connection between the peripheral and membrane domains. The peripheral domain assembly is stabilized by unique terminal extensions and an insertion loop. The membrane domain structure reveals novel dynamic features. Unusual conformation of the conserved interface between the peripheral and membrane domains suggests an uncoupled conformation of the complex. Considering constraints imposed by the structural data, we suggest a new simple hypothetical coupling mechanism for the molecular machine. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7nz1.cif.gz | 462.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7nz1.ent.gz | 366.4 KB | Display | PDB format |
PDBx/mmJSON format | 7nz1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7nz1_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7nz1_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7nz1_validation.xml.gz | 69.1 KB | Display | |
Data in CIF | 7nz1_validation.cif.gz | 113.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nz/7nz1 ftp://data.pdbj.org/pub/pdb/validation_reports/nz/7nz1 | HTTPS FTP |
-Related structure data
Related structure data | 12661MC 7nyhC 7nyrC 7nyuC 7nyvC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-NADH-quinone oxidoreductase subunit ... , 6 types, 6 molecules BDEFGI
#1: Protein | Mass: 25097.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli B (bacteria) / References: NADH:ubiquinone reductase (H+-translocating) |
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#2: Protein | Mass: 68321.945 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli B (bacteria) / Strain: BL21(AI) References: UniProt: P33599, NADH:ubiquinone reductase (H+-translocating) |
#3: Protein | Mass: 18630.049 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli B (bacteria) References: UniProt: P0AFD1, NADH:ubiquinone reductase (H+-translocating) |
#4: Protein | Mass: 49368.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli B (bacteria) References: UniProt: P31979, NADH:ubiquinone reductase (H+-translocating) |
#5: Protein | Mass: 100419.211 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli B (bacteria) References: UniProt: P33602, NADH:ubiquinone reductase (H+-translocating) |
#6: Protein | Mass: 20562.771 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli B (bacteria) References: UniProt: P0AFD6, NADH:ubiquinone reductase (H+-translocating) |
-Non-polymers , 5 types, 1181 molecules
#7: Chemical | ChemComp-SF4 / #8: Chemical | #9: Chemical | ChemComp-FMN / | #10: Chemical | ChemComp-CA / | #11: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Respiratory complex I from Escherichia coli - focused refinement of cytoplasmic arm Type: COMPLEX / Entity ID: #1-#6 / Source: NATURAL | ||||||||||||||||||||
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Molecular weight | Value: 0.28 MDa / Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Escherichia coli B (bacteria) / Strain: BL21(AI) / Cellular location: cell membrane | ||||||||||||||||||||
Buffer solution | pH: 6.8 Details: The buffer was used for gel filtration of protein reconstituted in lipid nanodiscs | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R0.6/1 | ||||||||||||||||||||
Vitrification | Instrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 97 % / Chamber temperature: 296 K |
-Electron microscopy imaging
Microscopy | Model: JEOL CRYO ARM 300 |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 60000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 900 nm / Cs: 2.55 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: JEOL CRYOSPECPORTER |
Image recording | Average exposure time: 3 sec. / Electron dose: 64.7 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 9122 |
EM imaging optics | Energyfilter name: In-column Omega Filter / Energyfilter slit width: 20 eV |
-Processing
Software |
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1256734 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 286333 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 30 / Protocol: AB INITIO MODEL / Space: REAL / Target criteria: Correlation coefficient | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 4HEA | ||||||||||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.33 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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