+Open data
-Basic information
Entry | Database: PDB / ID: 6oqu | ||||||
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Title | E. coli ATP synthase State 1d | ||||||
Components | (ATP synthase ...) x 8 | ||||||
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 ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / membrane => GO:0016020 / ADP binding ...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 ATP synthase complex, catalytic core F(1) / H+-transporting two-sector ATPase / proton-transporting ATPase activity, rotational mechanism / proton-transporting ATP synthase activity, rotational mechanism / membrane => GO:0016020 / ADP binding / hydrolase activity / lipid binding / ATP hydrolysis activity / ATP binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||
Authors | Stewart, A.G. / Sobti, M. / Walshe, J.L. | ||||||
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 | 6oqu.cif.gz | 806.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6oqu.ent.gz | 664.6 KB | Display | PDB format |
PDBx/mmJSON format | 6oqu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6oqu_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 6oqu_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 6oqu_validation.xml.gz | 115.8 KB | Display | |
Data in CIF | 6oqu_validation.cif.gz | 181.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oq/6oqu ftp://data.pdbj.org/pub/pdb/validation_reports/oq/6oqu | HTTPS FTP |
-Related structure data
Related structure data | 20170MC 6oqrC 6oqsC 6oqtC 6oqvC 6oqwC 6pqvC 6vwkC 6wnqC 6wnrC 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
-ATP synthase ... , 8 types, 22 molecules WCBAXYHGFEDJLMNOPQRISa
#1: Protein | Mass: 19289.061 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli / Gene: atpH, HMPREF1611_00658 / Production host: Escherichia coli (E. coli) / References: UniProt: V0ZA15, UniProt: P0ABA4*PLUS | ||||||||||||
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#2: Protein | Mass: 55281.871 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli / Gene: atpA, AD31_4476 / Production host: Escherichia coli (E. coli) References: UniProt: A0A073FQ32, UniProt: P0ABB0*PLUS, H+-transporting two-sector ATPase #3: Protein | Mass: 17257.889 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli / Gene: atpF, AD31_4478 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A073FPT7, UniProt: P0ABA0*PLUS #4: Protein | | Mass: 15087.244 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli / Gene: atpC, CCU01_030215 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4V1DSB5, UniProt: P0A6E6*PLUS #5: Protein | | Mass: 31539.285 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli / Gene: atpG, BN16_43751 / Production host: Escherichia coli (E. coli) / References: UniProt: J7RYJ3, UniProt: P0ABA6*PLUS #6: Protein | Mass: 51664.574 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli / Gene: atpD, CDCO157_4410 / Production host: Escherichia coli (E. coli) References: UniProt: A0A0F6CB56, UniProt: P0ABB4*PLUS, H+-transporting two-sector ATPase #7: 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 #8: 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 |
-Non-polymers , 4 types, 12 molecules
#9: Chemical | #10: Chemical | ChemComp-MG / #11: Chemical | #12: Chemical | ChemComp-PO4 / | |
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-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: E. coli ATP synthase / Type: COMPLEX / Entity ID: #1-#8 / Source: RECOMBINANT |
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Molecular weight | Value: 0.558 MDa / Experimental value: YES |
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 |
Specimen support | Details: unspecified |
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: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 33239 / Symmetry type: POINT | ||||||||||||||||||||||||
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