+Open data
-Basic information
Entry | Database: PDB / ID: 6vwk | ||||||
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Title | E. coli ATP Synthase ADP Sub-state 3a Fo Focussed | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / E coli ATP Synthase / ion channel / ATPase | ||||||
Function / homology | Function and homology information proton-transporting ATP synthase complex / proton motive force-driven plasma membrane ATP synthesis / proton-transporting ATP synthase complex, coupling factor F(o) / proton motive force-driven ATP synthesis / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / hydrolase activity / lipid binding / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||
Authors | Stewart, A.G. / Walshe, J.L. / Sobti, M. | ||||||
Funding support | Australia, 1items
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Citation | Journal: Nat Commun / Year: 2020 Title: Cryo-EM structures provide insight into how E. coli FF ATP synthase accommodates symmetry mismatch. Authors: Meghna Sobti / James L Walshe / Di Wu / Robert Ishmukhametov / Yi C Zeng / Carol V Robinson / Richard M Berry / Alastair G Stewart / Abstract: FF ATP synthase functions as a biological rotary generator that makes a major contribution to cellular energy production. It comprises two molecular motors coupled together by a central and a ...FF ATP synthase functions as a biological rotary generator that makes a major contribution to cellular energy production. It comprises two molecular motors coupled together by a central and a peripheral stalk. Proton flow through the F motor generates rotation of the central stalk, inducing conformational changes in the F motor that catalyzes ATP production. Here we present nine cryo-EM structures of E. coli ATP synthase to 3.1-3.4 Å resolution, in four discrete rotational sub-states, which provide a comprehensive structural model for this widely studied bacterial molecular machine. We observe torsional flexing of the entire complex and a rotational sub-step of F associated with long-range conformational changes that indicates how this flexibility accommodates the mismatch between the 3- and 10-fold symmetries of the F and F motors. We also identify density likely corresponding to lipid molecules that may contribute to the rotor/stator interaction within the F motor. | ||||||
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 | 6vwk.cif.gz | 191.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vwk.ent.gz | 154.3 KB | Display | PDB format |
PDBx/mmJSON format | 6vwk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6vwk_validation.pdf.gz | 734.8 KB | Display | wwPDB validaton report |
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Full document | 6vwk_full_validation.pdf.gz | 734.3 KB | Display | |
Data in XML | 6vwk_validation.xml.gz | 31.4 KB | Display | |
Data in CIF | 6vwk_validation.cif.gz | 50.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vw/6vwk ftp://data.pdbj.org/pub/pdb/validation_reports/vw/6vwk | HTTPS FTP |
-Related structure data
Related structure data | 21419MC 6oqrC 6oqsC 6oqtC 6oquC 6oqvC 6oqwC 6pqvC 6wnqC 6wnrC 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
#1: Protein | Mass: 8259.064 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: atpE, ECJG_03465 / Production host: Escherichia coli (E. coli) / References: UniProt: F4TL55, UniProt: P68699*PLUS #2: Protein | Mass: 17289.953 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: atpf / Production host: Escherichia coli (E. coli) / References: UniProt: D6IFY0, UniProt: P0ABA0*PLUS #3: Protein | | Mass: 30324.096 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: atpB / Production host: Escherichia coli (E. coli) / References: UniProt: C3SL77, UniProt: P0AB98*PLUS |
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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: E. coli ATP Synthase / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 0.558 MDa / Experimental value: NO |
Source (natural) | Organism: Escherichia coli (E. coli) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 8 |
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: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 48 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: dev_3758: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 78283 / Symmetry type: POINT | ||||||||||||||||||||||||
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