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 1.2 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: 10.1038/s41467-020-16387-2
  • Structures With Same Primary Citation

  • 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 ...

    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

    Faculty of Medicine, St Vincent's Clinical School, UNSW Sydney, Kensington, NSW, 2052, Australia. a.stewart@victorchang.edu.au.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ATP synthase subunit deltaW177Escherichia coliMutation(s): 0 
Gene Names: atpHHMPREF1611_00658
Find proteins for P0ABA4 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0ABA4
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ATP synthase subunit alphaA, B, C513Escherichia coliMutation(s): 0 
Gene Names: atpAAD31_4476
EC: 7.1.2.2
Find proteins for P0ABB0 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0ABB0
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
ATP synthase subunit bX, Y156Escherichia coliMutation(s): 0 
Gene Names: atpFAD31_4478
Find proteins for P0ABA0 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0ABA0
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  • Reference Sequence

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
ATP synthase epsilon chainH139Escherichia coliMutation(s): 0 
Gene Names: atpCCCU01_030215
Find proteins for P0A6E6 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0A6E6
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  • Reference Sequence

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
ATP synthase gamma chainG287Escherichia coliMutation(s): 0 
Gene Names: atpGBN16_43751
Find proteins for P0ABA6 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0ABA6
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  • Reference Sequence

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
ATP synthase subunit betaD, E, F471Escherichia coliMutation(s): 0 
Gene Names: atpDCDCO157_4410
EC: 7.1.2.2
Find proteins for P0ABB4 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0ABB4
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  • Reference Sequence

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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
ATP synthase subunit cI, J, L, M, N, O, P, Q, R, S79Escherichia coliMutation(s): 0 
Gene Names: atpEECJG_03465
Find proteins for P68699 (Escherichia coli (strain K12))
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Go to UniProtKB:  P68699
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  • Reference Sequence

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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
ATP synthase subunit aa271Escherichia coliMutation(s): 0 
Gene Names: atpB
Find proteins for P0AB98 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0AB98
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download CCD File 
A, B, C
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
ADP
Query on ADP

Download CCD File 
D, E, F
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
PO4
Query on PO4

Download CCD File 
D
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
MG
Query on MG

Download CCD File 
A, B, C, D, F
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
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 

  • 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