+Open data
-Basic information
Entry | Database: PDB / ID: 7vy1 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Membrane arm of deactive state CI from Q10 dataset | ||||||||||||
Components |
| ||||||||||||
Keywords | ELECTRON TRANSPORT / mammalian / mitochondrial / respiratory / complex I | ||||||||||||
Function / homology | Function and homology information Mitochondrial Fatty Acid Beta-Oxidation / Glyoxylate metabolism and glycine degradation / protein lipoylation / Mitochondrial protein import / Complex I biogenesis / Respiratory electron transport / cellular response to oxygen levels / Neutrophil degranulation / gliogenesis / neural precursor cell proliferation ...Mitochondrial Fatty Acid Beta-Oxidation / Glyoxylate metabolism and glycine degradation / protein lipoylation / Mitochondrial protein import / Complex I biogenesis / Respiratory electron transport / cellular response to oxygen levels / Neutrophil degranulation / gliogenesis / neural precursor cell proliferation / [2Fe-2S] cluster assembly / mitochondrial large ribosomal subunit / oxygen sensor activity / NADH:ubiquinone reductase (H+-translocating) / mitochondrial respiratory chain complex I / mitochondrial electron transport, NADH to ubiquinone / mitochondrial respiratory chain complex I assembly / NADH dehydrogenase (ubiquinone) activity / quinone binding / ATP synthesis coupled electron transport / respirasome / aerobic respiration / reactive oxygen species metabolic process / electron transport chain / mitochondrial intermembrane space / fatty acid biosynthetic process / NAD binding / 4 iron, 4 sulfur cluster binding / response to oxidative stress / mitochondrial inner membrane / membrane => GO:0016020 / mitochondrial matrix / nuclear speck / ubiquitin protein ligase binding / endoplasmic reticulum / mitochondrion / nucleoplasm / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Sus scrofa (pig) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||||||||
Authors | Gu, J.K. / Yang, M.J. | ||||||||||||
Funding support | China, 3items
| ||||||||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2022 Title: The coupling mechanism of mammalian mitochondrial complex I. Authors: Jinke Gu / Tianya Liu / Runyu Guo / Laixing Zhang / Maojun Yang / Abstract: Mammalian respiratory complex I (CI) is a 45-subunit, redox-driven proton pump that generates an electrochemical gradient across the mitochondrial inner membrane to power ATP synthesis in ...Mammalian respiratory complex I (CI) is a 45-subunit, redox-driven proton pump that generates an electrochemical gradient across the mitochondrial inner membrane to power ATP synthesis in mitochondria. In the present study, we report cryo-electron microscopy structures of CI from Sus scrofa in six treatment conditions at a resolution of 2.4-3.5 Å, in which CI structures of each condition can be classified into two biochemical classes (active or deactive), with a notably higher proportion of active CI particles. These structures illuminate how hydrophobic ubiquinone-10 (Q10) with its long isoprenoid tail is bound and reduced in a narrow Q chamber comprising four different Q10-binding sites. Structural comparisons of active CI structures from our decylubiquinone-NADH and rotenone-NADH datasets reveal that Q10 reduction at site 1 is not coupled to proton pumping in the membrane arm, which might instead be coupled to Q10 oxidation at site 2. Our data overturn the widely accepted previous proposal about the coupling mechanism of CI. | ||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7vy1.cif.gz | 976.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7vy1.ent.gz | 792.3 KB | Display | PDB format |
PDBx/mmJSON format | 7vy1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vy/7vy1 ftp://data.pdbj.org/pub/pdb/validation_reports/vy/7vy1 | HTTPS FTP |
---|
-Related structure data
Related structure data | 32191MC 7v2cC 7v2dC 7v2eC 7v2fC 7v2hC 7v2kC 7v2rC 7v30C 7v31C 7v32C 7v33C 7v3mC 7vb7C 7vblC 7vbnC 7vbpC 7vbzC 7vc0C 7vwjC 7vwlC 7vxpC 7vxsC 7vxuC 7vy8C 7vy9C 7vyaC 7vyeC 7vyfC 7vygC 7vyhC 7vyiC 7vynC 7vysC 7vz1C 7vz8C 7vzvC 7vzwC 7w00C 7w0hC 7w0rC 7w0yC 7w1oC 7w1pC 7w1tC 7w1uC 7w1vC 7w1zC 7w20C 7w2kC 7w2lC 7w2rC 7w2uC 7w2yC 7w31C 7w32C 7w35C 7w4cC 7w4dC 7w4eC 7w4fC 7w4gC 7w4jC 7w4kC 7w4lC 7w4mC 7w4nC 7w4qC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-NADH dehydrogenase ... , 18 types, 18 molecules QSUVWYZabcdghnpuvw
#1: Protein | Mass: 53735.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1S1A8 |
---|---|
#2: Protein | Mass: 8088.424 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: K7GR43 |
#3: Protein | Mass: 9225.567 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RNI5 |
#4: Protein | Mass: 14686.894 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LGM4 |
#5: Protein | Mass: 16911.611 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1S6Q1 |
#7: Protein | Mass: 11939.366 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1V766 |
#8: Protein | Mass: 11128.515 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287AS93 |
#9: Protein | Mass: 21587.006 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SGC6 |
#10: Protein | Mass: 15603.177 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q2EN80 |
#11: Protein | Mass: 21702.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RWL7 |
#12: Protein | Mass: 20944.768 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1VYV0 |
#15: Protein | Mass: 14327.655 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A480JRW3 |
#16: Protein | Mass: 12506.591 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SV23 |
#22: Protein | Mass: 7044.278 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SD73 |
#24: Protein | Mass: 21864.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1T0A8 |
#27: Protein | Mass: 20064.096 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SLR1 |
#28: Protein | Mass: 16356.690 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SCH1 |
#29: Protein | Mass: 40476.082 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SIS9 |
-Protein , 5 types, 5 molecules Xefjo
#6: Protein | Mass: 17308.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287AAR5 |
---|---|
#13: Protein | Mass: 17384.729 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287BMW6 |
#14: Protein | Mass: 8664.053 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A1XQS6 |
#18: Protein | Mass: 12798.257 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: O79880 |
#23: Protein | Mass: 15117.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1T6M0 |
-NADH-ubiquinone oxidoreductase chain ... , 6 types, 6 molecules iklmrs
#17: Protein | Mass: 39077.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) References: UniProt: O79875, NADH:ubiquinone reductase (H+-translocating) |
---|---|
#19: Protein | Mass: 10827.253 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) References: UniProt: P56632, NADH:ubiquinone reductase (H+-translocating) |
#20: Protein | Mass: 68267.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) References: UniProt: Q71K68, NADH:ubiquinone reductase (H+-translocating) |
#21: Protein | Mass: 19021.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) References: UniProt: O79882, NADH:ubiquinone reductase (H+-translocating) |
#25: Protein | Mass: 51853.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) References: UniProt: Q7IIB7, NADH:ubiquinone reductase (H+-translocating) |
#26: Protein | Mass: 35667.520 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) References: UniProt: O79874, NADH:ubiquinone reductase (H+-translocating) |
-Non-polymers , 6 types, 24 molecules
#30: Chemical | ChemComp-PEE / #31: Chemical | ChemComp-CDL / #32: Chemical | ChemComp-8Q1 / | #33: Chemical | ChemComp-PLX / ( #34: Chemical | ChemComp-UQ / | #35: Chemical | ChemComp-ADP / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Respiratory complex I / Type: COMPLEX Entity ID: #1-#2, #5, #7-#8, #10-#12, #14-#16, #19, #23-#24, #27 Source: NATURAL |
---|---|
Source (natural) | Organism: Sus scrofa (pig) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1800 nm / Nominal defocus min: 1300 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
---|---|
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 193234 / Symmetry type: POINT |