8SPW | pdb_00008spw

PS3 F1 Rotorless, low ATP


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8SPW

This is version 1.3 of the entry. See complete history

Literature

The series of conformational states adopted by rotorless F 1 -ATPase during its hydrolysis cycle.

Sobti, M.Ueno, H.Brown, S.H.J.Noji, H.Stewart, A.G.

(2024) Structure 32: 393

  • DOI: https://doi.org/10.1016/j.str.2023.12.014
  • Primary Citation Related Structures: 
    8SPV, 8SPW, 8SPX

  • PubMed Abstract: 

    F 1 F o ATP synthase interchanges phosphate transfer energy and proton motive force via a rotary catalytic mechanism and isolated F 1 -ATPase subcomplexes can also hydrolyze ATP to generate rotation of their central γ rotor subunit. As ATP is hydrolyzed, the F 1 -ATPase cycles through a series of conformational states that mediates unidirectional rotation of the rotor. However, even in the absence of a rotor, the α and β subunits are still able to pass through a series of conformations, akin to those that generate rotation. Here, we use cryoelectron microscopy to establish the structures of these rotorless states. These structures indicate that cooperativity in this system is likely mediated by contacts between the β subunit lever domains, irrespective of the presence of the γ rotor subunit. These findings provide insight into how long-range information may be transferred in large biological systems.


  • Organizational Affiliation
    • Molecular, Structural and Computational Biology Division, The Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia; St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Kensington, NSW, Australia.

Macromolecule Content 

  • Total Structure Weight: 313.35 kDa 
  • Atom Count: 21,960 
  • Modeled Residue Count: 2,835 
  • Deposited Residue Count: 2,841 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP synthase subunit alpha
A, B, C
476Bacillus sp. PS3Mutation(s): 0 
Gene Names: uncAatpA
EC: 7.1.2.2
UniProt
Find proteins for A0A0M3VGF9 (Bacillus sp. (strain PS3))
Explore A0A0M3VGF9 
Go to UniProtKB:  A0A0M3VGF9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0M3VGF9
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP synthase subunit beta
D, E, F
471Bacillus sp. PS3Mutation(s): 0 
Gene Names: uncD
EC: 7.1.2.2
UniProt
Find proteins for P07677 (Bacillus sp. (strain PS3))
Explore P07677 
Go to UniProtKB:  P07677
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07677
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP

Query on ATP



Download:Ideal Coordinates CCD File
G [auth A],
I [auth B],
K [auth C],
M [auth D]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP

Query on ADP



Download:Ideal Coordinates CCD File
O [auth E]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
PO4

Query on PO4



Download:Ideal Coordinates CCD File
P [auth E]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
MG

Query on MG



Download:Ideal Coordinates CCD File
H [auth A],
J [auth B],
L [auth C],
N [auth D],
Q [auth E]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



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: 2024-01-24
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Database references
  • Version 1.2: 2024-04-17
    Changes: Database references
  • Version 1.3: 2025-05-28
    Changes: Data collection, Structure summary