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 6VWK | pdb_00006vwk

E. coli ATP Synthase ADP Sub-state 3a Fo Focussed


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 6VWK

This is version 1.4 of the entry. See complete history. 

Literature

Cryo-EM structures provide insight into how E. coli F1FoATP synthase accommodates symmetry mismatch.

Sobti, M., Walshe, J.L., Wu, D., Ishmukhametov, R., Zeng, Y.C., Robinson, C.V., Berry, R.M., Stewart, A.G.

(2020) Nat Commun 11: 2615-2615

  • DOI: https://doi.org/10.1038/s41467-020-16387-2
  • Primary Citation Related Structures: 
    6OQR, 6OQS, 6OQT, 6OQU, 6OQV, 6OQW, 6PQV, 6VWK, 6WNQ, 6WNR

  • PubMed Abstract: 

    F 1 F o 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 o motor generates rotation of the central stalk, inducing conformational changes in the F 1 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 o associated with long-range conformational changes that indicates how this flexibility accommodates the mismatch between the 3- and 10-fold symmetries of the F 1 and F o motors. We also identify density likely corresponding to lipid molecules that may contribute to the rotor/stator interaction within the F o motor.


  • Organizational Affiliation: 
    • Molecular, Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Darlinghurst, NSW, 2010, Australia.

Macromolecule Content 

  • Total Structure Weight: 147.49 kDa 
  • Atom Count: 8,423 
  • Modeled Residue Count: 1,133 
  • Deposited Residue Count: 1,373 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP synthase subunit c79Escherichia coliMutation(s): 0 
Gene Names: atpE, ECJG_03465
Membrane Entity: Yes 
UniProt
Find proteins for P68699 (Escherichia coli (strain K12))
Explore P68699 
Go to UniProtKB:  P68699
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68699
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP synthase subunit bK [auth X],
L [auth Y]
156Escherichia coliMutation(s): 0 
Gene Names: atpf
Membrane Entity: Yes 
UniProt
Find proteins for P0ABA0 (Escherichia coli (strain K12))
Explore P0ABA0 
Go to UniProtKB:  P0ABA0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ABA0
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP synthase subunit aM [auth a]271Escherichia coliMutation(s): 0 
Gene Names: atpB
Membrane Entity: Yes 
UniProt
Find proteins for P0AB98 (Escherichia coli (strain K12))
Explore P0AB98 
Go to UniProtKB:  P0AB98
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AB98
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia--

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-03
    Type: Initial release
  • Version 1.1: 2020-06-10
    Changes: Database references
  • Version 1.2: 2020-06-24
    Changes: Data processing, Structure summary
  • Version 1.3: 2024-03-06
    Changes: Data collection, Database references
  • Version 1.4: 2025-05-28
    Changes: Data collection, Structure summary