6N30 | pdb_00006n30

Bacillus PS3 ATP synthase class 3


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

Validation slider image for 6N30

This is version 1.2 of the entry. See complete history

Literature

Structure of a bacterial ATP synthase.

Guo, H.Suzuki, T.Rubinstein, J.L.

(2019) Elife 8

  • DOI: https://doi.org/10.7554/eLife.43128
  • Primary Citation Related Structures: 
    6N2D, 6N2Y, 6N2Z, 6N30

  • PubMed Abstract: 

    ATP synthases produce ATP from ADP and inorganic phosphate with energy from a transmembrane proton motive force. Bacterial ATP synthases have been studied extensively because they are the simplest form of the enzyme and because of the relative ease of genetic manipulation of these complexes. We expressed the Bacillus PS3 ATP synthase in Eschericia coli , purified it, and imaged it by cryo-EM, allowing us to build atomic models of the complex in three rotational states. The position of subunit ε shows how it is able to inhibit ATP hydrolysis while allowing ATP synthesis. The architecture of the membrane region shows how the simple bacterial ATP synthase is able to perform the same core functions as the equivalent, but more complicated, mitochondrial complex. The structures reveal the path of transmembrane proton translocation and provide a model for understanding decades of biochemical analysis interrogating the roles of specific residues in the enzyme.


  • Organizational Affiliation
    • The Hospital for Sick Children Research Institute, Toronto, Canada.

Macromolecule Content 

  • Total Structure Weight: 526.6 kDa 
  • Atom Count: 34,851 
  • Modeled Residue Count: 4,711 
  • Deposited Residue Count: 4,814 
  • Unique protein chains: 9

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Bacillus PS3 ATP synthase subunit bA [auth b2]168Bacillus sp. PS3Mutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Bacillus PS3 ATP synthase subunit bB [auth b1]168Bacillus sp. PS3Mutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Bacillus PS3 ATP synthase subunit aC [auth a]237Bacillus sp. PS3Mutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP synthase subunit c72Bacillus sp. PS3Mutation(s): 0 
Gene Names: atpEuncE
Membrane Entity: Yes 
UniProt
Find proteins for P00845 (Bacillus sp. (strain PS3))
Explore P00845 
Go to UniProtKB:  P00845
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00845
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP synthase subunit alphaN [auth C],
O [auth A],
P [auth B]
502Bacillus sp. PS3Mutation(s): 0 
Gene Names: uncAatpA
EC: 3.6.3.14 (PDB Primary Data), 7.1.2.2 (UniProt)
Membrane Entity: Yes 
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
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP synthase subunit betaQ [auth F],
R [auth D],
S [auth E]
473Bacillus sp. PS3Mutation(s): 0 
Gene Names: uncDatpD
EC: 3.6.3.14 (PDB Primary Data), 7.1.2.2 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for A0A0M4U1P9 (Bacillus sp. (strain PS3))
Explore A0A0M4U1P9 
Go to UniProtKB:  A0A0M4U1P9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0M4U1P9
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP synthase gamma chainT [auth G]285Bacillus sp. PS3Mutation(s): 0 
Gene Names: uncGatpG
Membrane Entity: Yes 
UniProt
Find proteins for A0A0M4TPJ7 (Bacillus sp. (strain PS3))
Explore A0A0M4TPJ7 
Go to UniProtKB:  A0A0M4TPJ7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0M4TPJ7
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP synthase epsilon chainU [auth H]133Bacillus sp. PS3Mutation(s): 0 
Gene Names: uncCatpC
Membrane Entity: Yes 
UniProt
Find proteins for A0A0M5MQR7 (Bacillus sp. (strain PS3))
Explore A0A0M5MQR7 
Go to UniProtKB:  A0A0M5MQR7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0M5MQR7
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Bacillus PS3 ATP synthase subunit deltaV [auth I]178Bacillus sp. PS3Mutation(s): 0 

Small Molecules

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

Query on ATP



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

Query on ADP



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

Query on PO4



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

Query on MG



Download:Ideal Coordinates CCD File
BA [auth B],
EA [auth E],
X [auth C],
Z [auth A]
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 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.14
RECONSTRUCTIONcryoSPARC2.0

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)CanadaMOP 81294
Japan Society for the Promotion of Science (JSPS)JapanJP18H02409

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-20
    Type: Initial release
  • Version 1.1: 2020-01-15
    Changes: Author supporting evidence
  • Version 1.2: 2024-12-25
    Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary