9AVJ | pdb_00009avj

PS3 F1 ATPase Wild type


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.72 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

The molecular structure of an axle-less F 1 -ATPase.

Furlong, E.J.Reininger-Chatzigiannakis, I.P.Zeng, Y.C.Brown, S.H.J.Sobti, M.Stewart, A.G.

(2024) Biochim Biophys Acta Bioenerg 1866: 149521-149521

  • DOI: https://doi.org/10.1016/j.bbabio.2024.149521
  • Primary Citation Related Structures: 
    8U1H, 9AVJ

  • PubMed Abstract: 

    F 1 F o ATP synthase is a molecular rotary motor that can generate ATP using a transmembrane proton motive force. Isolated F 1 -ATPase catalytic cores can hydrolyse ATP, passing through a series of conformational states involving rotation of the central γ rotor subunit and the opening and closing of the catalytic β subunits. Cooperativity in F 1 -ATPase has long thought to be conferred through the γ subunit, with three key interaction sites between the γ and β subunits being identified. Single molecule studies have demonstrated that the F 1 complexes lacking the γ axle still "rotate" and hydrolyse ATP, but with less efficiency. We solved the cryogenic electron microscopy structure of an axle-less Bacillus sp. PS3 F 1 -ATPase. The unexpected binding-dwell conformation of the structure in combination with the observed lack of interactions between the axle-less γ and the open β subunit suggests that the complete γ subunit is important for coordinating efficient ATP binding of F 1 -ATPase.


  • Organizational Affiliation
    • Molecular, Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Darlinghurst, Australia; Division of Biomedical Science and Biochemistry, Research School of Biology, Australian National University, Acton, ACT, Australia.

Macromolecule Content 

  • Total Structure Weight: 344.36 kDa 
  • Atom Count: 23,188 
  • Modeled Residue Count: 2,988 
  • Deposited Residue Count: 3,118 
  • Unique protein chains: 7

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP synthase subunit alpha474Bacillus sp. PS3Mutation(s): 0 
Gene Names: uncAatpA
EC: 7.1.2.2
UniProt
Find proteins for P09219 (Bacillus sp. (strain PS3))
Explore P09219 
Go to UniProtKB:  P09219
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UniProt GroupP09219
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP synthase subunit alpha475Bacillus sp. PS3Mutation(s): 0 
Gene Names: uncAatpA
EC: 7.1.2.2
UniProt
Find proteins for P09219 (Bacillus sp. (strain PS3))
Explore P09219 
Go to UniProtKB:  P09219
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UniProt GroupP09219
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP synthase subunit alpha476Bacillus sp. PS3Mutation(s): 0 
Gene Names: uncAatpA
EC: 7.1.2.2
UniProt
Find proteins for P09219 (Bacillus sp. (strain PS3))
Explore P09219 
Go to UniProtKB:  P09219
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UniProt GroupP09219
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP synthase subunit beta470Bacillus sp. PS3Mutation(s): 0 
Gene Names: uncDatpD
EC: 7.1.2.2
UniProt
Find proteins for P07677 (Bacillus sp. (strain PS3))
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Go to UniProtKB:  P07677
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UniProt GroupP07677
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP synthase subunit beta470Bacillus sp. PS3Mutation(s): 0 
Gene Names: uncDatpD
EC: 7.1.2.2
UniProt
Find proteins for P07677 (Bacillus sp. (strain PS3))
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP synthase subunit beta471Bacillus sp. PS3Mutation(s): 0 
Gene Names: uncDatpD
EC: 7.1.2.2
UniProt
Find proteins for P07677 (Bacillus sp. (strain PS3))
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Go to UniProtKB:  P07677
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UniProt GroupP07677
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP synthase gamma chain282Bacillus sp. PS3Mutation(s): 0 
Gene Names: uncGatpG
UniProt
Find proteins for P09222 (Bacillus sp. (strain PS3))
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ANP

Query on ANP



Download:Ideal Coordinates CCD File
H [auth A],
J [auth B],
L [auth C],
N [auth D],
P [auth F]
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
I [auth A],
K [auth B],
M [auth C],
O [auth D],
Q [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.72 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: 2024-10-30
    Type: Initial release
  • Version 1.1: 2024-11-20
    Changes: Data collection, Database references
  • Version 1.2: 2025-05-21
    Changes: Data collection