[English] 日本語
Yorodumi- PDB-8dh6: Cryo-EM structure of Saccharomyces cerevisiae cytochrome c oxidas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8dh6 | ||||||
---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of Saccharomyces cerevisiae cytochrome c oxidase (Complex IV) extracted in lipid nanodiscs | ||||||
Components | (Cytochrome c oxidase subunit ...) x 9 | ||||||
Keywords | MEMBRANE PROTEIN / cytochrome c oxidase / Complex IV | ||||||
Function / homology | Function and homology information mitochondrial cytochrome c oxidase assembly / mitochondrial respiratory chain complex IV / cytochrome-c oxidase / cellular respiration / mitochondrial electron transport, cytochrome c to oxygen / electron transport coupled proton transport / cytochrome-c oxidase activity / ATP synthesis coupled electron transport / aerobic respiration / proton transmembrane transport ...mitochondrial cytochrome c oxidase assembly / mitochondrial respiratory chain complex IV / cytochrome-c oxidase / cellular respiration / mitochondrial electron transport, cytochrome c to oxygen / electron transport coupled proton transport / cytochrome-c oxidase activity / ATP synthesis coupled electron transport / aerobic respiration / proton transmembrane transport / mitochondrial membrane / mitochondrial intermembrane space / mitochondrial inner membrane / oxidoreductase activity / copper ion binding / heme binding / mitochondrion / zinc ion binding / metal ion binding Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.94 Å | ||||||
Authors | Godoy, A.S. / Song, Y. / Cheruvara, H. / Quigley, A. / Oliva, G. | ||||||
Funding support | Brazil, 1items
| ||||||
Citation | Journal: To Be Published Title: Cryo-EM structure of Saccharomyces cerevisiae cytochrome c oxidase (Complex IV) extracted in lipid nanodiscs Authors: Godoy, A.S. / Song, Y. / Cheruvara, H. / Quigley, A. / Oliva, G. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8dh6.cif.gz | 296 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8dh6.ent.gz | 236.4 KB | Display | PDB format |
PDBx/mmJSON format | 8dh6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dh/8dh6 ftp://data.pdbj.org/pub/pdb/validation_reports/dh/8dh6 | HTTPS FTP |
---|
-Related structure data
Related structure data | 27430MC 8dh7C 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
-Cytochrome c oxidase subunit ... , 9 types, 9 molecules abcdefghi
#1: Protein | Mass: 58832.586 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P00401, cytochrome-c oxidase |
---|---|
#2: Protein | Mass: 26779.816 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P00410, cytochrome-c oxidase |
#3: Protein | Mass: 30383.582 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P00420, cytochrome-c oxidase |
#4: Protein | Mass: 14188.949 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P04037 |
#5: Protein | Mass: 14891.784 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P00424 |
#6: Protein | Mass: 12641.998 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P00427 |
#7: Protein | Mass: 6811.154 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P10174 |
#8: Protein | Mass: 5737.735 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P04039 |
#9: Protein | Mass: 6471.684 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P07255 |
-Non-polymers , 6 types, 17 molecules
#10: Chemical | ChemComp-CA / | ||||||
---|---|---|---|---|---|---|---|
#11: Chemical | ChemComp-MG / | ||||||
#12: Chemical | #13: Chemical | #14: Chemical | ChemComp-PEF / #15: Chemical | ChemComp-ZN / | |
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Complex IVCytochrome c oxidase / Type: COMPLEX / Entity ID: #1-#9 / Source: NATURAL |
---|---|
Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Buffer solution | pH: 7 |
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: 3200 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 1.011775103 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 247631 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
|