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Yorodumi- PDB-6wti: The Cryo-EM structure of the ubiquinol oxidase from Escherichia coli -
+Open data
-Basic information
Entry | Database: PDB / ID: 6wti | ||||||
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Title | The Cryo-EM structure of the ubiquinol oxidase from Escherichia coli | ||||||
Components |
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Keywords | OXIDOREDUCTASE / ubiquinol oxidase cytochrome bo3 / membrane protein | ||||||
Function / homology | Function and homology information cytochrome bo3 ubiquinol oxidase activity => GO:0009486 / 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 / ubiquinone binding ...cytochrome bo3 ubiquinol oxidase activity => GO:0009486 / 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 / ubiquinone binding / electron transport coupled proton transport / : / ATP synthesis coupled electron transport / respiratory electron transport chain / aerobic respiration / membrane => GO:0016020 / electron transfer activity / copper ion binding / heme binding / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.38 Å | ||||||
Authors | Su, C.-C. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Methods / Year: 2021 Title: A 'Build and Retrieve' methodology to simultaneously solve cryo-EM structures of membrane proteins. Authors: Chih-Chia Su / Meinan Lyu / Christopher E Morgan / Jani Reddy Bolla / Carol V Robinson / Edward W Yu / Abstract: Single-particle cryo-electron microscopy (cryo-EM) has become a powerful technique in the field of structural biology. However, the inability to reliably produce pure, homogeneous membrane protein ...Single-particle cryo-electron microscopy (cryo-EM) has become a powerful technique in the field of structural biology. However, the inability to reliably produce pure, homogeneous membrane protein samples hampers the progress of their structural determination. Here, we develop a bottom-up iterative method, Build and Retrieve (BaR), that enables the identification and determination of cryo-EM structures of a variety of inner and outer membrane proteins, including membrane protein complexes of different sizes and dimensions, from a heterogeneous, impure protein sample. We also use the BaR methodology to elucidate structural information from Escherichia coli K12 crude membrane and raw lysate. The findings demonstrate that it is possible to solve high-resolution structures of a number of relatively small (<100 kDa) and less abundant (<10%) unidentified membrane proteins within a single, heterogeneous sample. Importantly, these results highlight the potential of cryo-EM for systems structural proteomics. | ||||||
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 | 6wti.cif.gz | 236.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6wti.ent.gz | 183.2 KB | Display | PDB format |
PDBx/mmJSON format | 6wti.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6wti_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 6wti_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 6wti_validation.xml.gz | 43.4 KB | Display | |
Data in CIF | 6wti_validation.cif.gz | 61.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wt/6wti ftp://data.pdbj.org/pub/pdb/validation_reports/wt/6wti | HTTPS FTP |
-Related structure data
Related structure data | 21897MC 6wtzC 6wu0C 6wu6C 7jz2C 7jz3C 7jz6C 7jzhC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Cytochrome o ubiquinol oxidase, subunit ... , 2 types, 2 molecules AD
#1: Protein | Mass: 74424.469 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cyoB, ECDEC2C_0430 / Production host: Escherichia coli (E. coli) References: UniProt: H4KCU1, UniProt: P0ABI8*PLUS, Oxidoreductases; Acting on diphenols and related substances as donors; With oxygen as acceptor |
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#4: Protein | Mass: 12037.402 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cyoD, EC12741_3890 / Production host: Escherichia coli (E. coli) References: UniProt: I2RK84, UniProt: P0ABJ6*PLUS, Oxidoreductases; Acting on diphenols and related substances as donors; With oxygen as acceptor |
-Protein , 2 types, 2 molecules BC
#2: Protein | Mass: 34947.203 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: cyoA / Production host: Escherichia coli (E. coli) / References: UniProt: A0A024L5V9, UniProt: P0ABJ1*PLUS |
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#3: Protein | Mass: 22642.566 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ECDG_00226 / Production host: Escherichia coli (E. coli) / References: UniProt: D6I7E4, UniProt: P0ABJ3*PLUS |
-Non-polymers , 6 types, 14 molecules
#5: Chemical | ChemComp-HEM / | ||
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#6: Chemical | ChemComp-HEO / | ||
#7: Chemical | ChemComp-CU / | ||
#8: Chemical | ChemComp-UQ8 / | ||
#9: Chemical | ChemComp-3PE / #10: Chemical | ChemComp-U9V / | |
-Details
Has ligand of interest | Y |
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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: ubiquinol oxidase / Type: COMPLEX / Entity ID: #1-#4 / Source: RECOMBINANT |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 0.5 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 R1.2/1.3 |
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: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 2.38 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 334222 / Symmetry type: POINT |