6OQU

E. coli ATP synthase State 1d


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 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 of 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.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit deltaA [auth W]177Escherichia coliMutation(s): 0 
Gene Names: atpHHMPREF1611_00658
Membrane Entity: Yes 
UniProt
Find proteins for P0ABA4 (Escherichia coli (strain K12))
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UniProt GroupP0ABA4
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit alphaB [auth C],
C [auth B],
D [auth A]
513Escherichia coliMutation(s): 0 
Gene Names: atpAAD31_4476
EC: 7.1.2.2
Membrane Entity: Yes 
UniProt
Find proteins for P0ABB0 (Escherichia coli (strain K12))
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UniProt GroupP0ABB0
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit bE [auth X],
S [auth Y]
156Escherichia coliMutation(s): 0 
Gene Names: atpFAD31_4478
Membrane Entity: Yes 
UniProt
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UniProt GroupP0ABA0
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase epsilon chainF [auth H]139Escherichia coliMutation(s): 0 
Gene Names: atpCCCU01_030215
Membrane Entity: Yes 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase gamma chain287Escherichia coliMutation(s): 0 
Gene Names: atpGBN16_43751
Membrane Entity: Yes 
UniProt
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UniProt GroupP0ABA6
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit betaH [auth F],
I [auth E],
J [auth D]
471Escherichia coliMutation(s): 0 
Gene Names: atpDCDCO157_4410
EC: 7.1.2.2
Membrane Entity: Yes 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit c79Escherichia coliMutation(s): 0 
Gene Names: atpEECJG_03465
Membrane Entity: Yes 
UniProt
Find proteins for P68699 (Escherichia coli (strain K12))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
ATP synthase subunit aT [auth a]271Escherichia coliMutation(s): 0 
Gene Names: atpB
Membrane Entity: Yes 
UniProt
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
AA [auth A],
W [auth C],
Y [auth B]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP
Query on ADP

Download Ideal Coordinates CCD File 
CA [auth F],
EA [auth E],
FA [auth D]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
GA [auth D]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
MG
Query on MG

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BA [auth A],
DA [auth F],
HA [auth D],
X [auth C],
Z [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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: 2024-03-20
    Changes: Data collection, Database references, Derived calculations