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Yorodumi- PDB-8go3: Cryo-EM structure of Escherichia coli cytochrome bo3 in DDM detergent -
+Open data
-Basic information
Entry | Database: PDB / ID: 8go3 | ||||||
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Title | Cryo-EM structure of Escherichia coli cytochrome bo3 in DDM detergent | ||||||
Components |
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Keywords | TRANSLOCASE / Cytochrome bo3 / ubiquinol oxidase / DDM detergent | ||||||
Function / homology | Function and homology information cytochrome o ubiquinol oxidase complex / oxidoreduction-driven active transmembrane transporter activity / ubiquinol oxidase (H+-transporting) / cytochrome bo3 ubiquinol oxidase activity / aerobic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / cytochrome-c oxidase activity / proton transmembrane transporter activity / : / electron transport coupled proton transport ...cytochrome o ubiquinol oxidase complex / oxidoreduction-driven active transmembrane transporter activity / ubiquinol oxidase (H+-transporting) / cytochrome bo3 ubiquinol oxidase activity / aerobic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / cytochrome-c oxidase activity / proton transmembrane transporter activity / : / electron transport coupled proton transport / ATP synthesis coupled electron transport / aerobic respiration / electron transfer activity / copper ion binding / heme binding / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli K-12 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.09 Å | ||||||
Authors | Cao, H.Y. / Li, K. / Li, C.Y. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Cryo-EM structure of Escherichia coli cytochrome bo3 in DDM detergent Authors: Cao, H.Y. / Li, K. / Li, C.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8go3.cif.gz | 228.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8go3.ent.gz | 177.3 KB | Display | PDB format |
PDBx/mmJSON format | 8go3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8go3_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 8go3_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 8go3_validation.xml.gz | 53.4 KB | Display | |
Data in CIF | 8go3_validation.cif.gz | 75.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/go/8go3 ftp://data.pdbj.org/pub/pdb/validation_reports/go/8go3 | HTTPS FTP |
-Related structure data
Related structure data | 34171MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Cytochrome bo(3) ubiquinol oxidase subunit ... , 3 types, 3 molecules ABD
#1: Protein | Mass: 74424.469 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: S88 / ExPEC References: UniProt: B7MD89, ubiquinol oxidase (H+-transporting) |
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#2: Protein | Mass: 34947.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / Strain: K12 / References: UniProt: P0ABJ1 |
#4: Protein | Mass: 12037.402 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: C3TLX2 |
-Protein , 1 types, 1 molecules C
#3: Protein | Mass: 22642.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli K-12 (bacteria) / References: UniProt: B6HZN6 |
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-Non-polymers , 5 types, 6 molecules
#5: Chemical | ChemComp-HEM / |
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#6: Chemical | ChemComp-HEO / |
#7: Chemical | ChemComp-CU / |
#8: Chemical | ChemComp-UQ8 / |
#9: Chemical |
-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: Purified Escherichia coli cytochrome bo3 / Type: COMPLEX / Entity ID: #1-#4 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Escherichia coli K-12 (bacteria) |
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 |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm |
Image recording | Electron dose: 50.2 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.09 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 538627 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 73.87 Å2 | ||||||||||||||||||||||||
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