6N2Y

Bacillus PS3 ATP synthase class 1

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Structure of a bacterial ATP synthase.

Guo, H., Suzuki, T., Rubinstein, J.L.

(2019) Elife 8: --

  • DOI: 10.7554/eLife.43128
  • Primary Citation of Related Structures:  

  • 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 o ...

    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: 

    Department of Medical Biophysics, The University of Toronto, Toronto, Canada.,Department of Molecular Bioscience, Kyoto-Sangyo University, Kyoto, Japan.,The Hospital for Sick Children Research Institute, Toronto, Canada.,Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan.,Department of Biochemistry, The University of Toronto, Toronto, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ATP synthase subunit alpha
A, B, C
502Bacillus sp. (strain PS3)Mutation(s): 0 
Gene Names: uncA (atpA)
EC: 7.1.2.2
Membrane protein
mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
F-type ATPase		Protein: 
F1Fo synthase, class 1
Find proteins for A0A0M3VGF9 (Bacillus sp. (strain PS3))
Go to UniProtKB:  A0A0M3VGF9
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ATP synthase subunit beta
D, E, F
473Bacillus sp. (strain PS3)Mutation(s): 0 
Gene Names: uncD (atpD)
EC: 7.1.2.2
Membrane protein
mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
F-type ATPase		Protein: 
F1Fo synthase, class 1
Find proteins for A0A0M4U1P9 (Bacillus sp. (strain PS3))
Go to UniProtKB:  A0A0M4U1P9
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
ATP synthase gamma chain
G
285Bacillus sp. (strain PS3)Mutation(s): 0 
Gene Names: uncG (atpG)
Membrane protein
mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
F-type ATPase		Protein: 
F1Fo synthase, class 1
Find proteins for A0A0M4TPJ7 (Bacillus sp. (strain PS3))
Go to UniProtKB:  A0A0M4TPJ7
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
ATP synthase epsilon chain
H
133Bacillus sp. (strain PS3)Mutation(s): 0 
Gene Names: uncC (atpC)
Membrane protein
mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
F-type ATPase		Protein: 
F1Fo synthase, class 1
Find proteins for A0A0M5MQR7 (Bacillus sp. (strain PS3))
Go to UniProtKB:  A0A0M5MQR7
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
ATP synthase subunit delta
I
178N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
ATP synthase subunit b
b2
168N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
ATP synthase subunit b
b1
168N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
ATP synthase subunit a
a
237N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
ATP synthase subunit c
c0, c1, c2, c3, c4, c5, c6, c7, c8, c9
72Bacillus sp. (strain PS3)Mutation(s): 0 
Gene Names: atpE (uncE)
Membrane protein
mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
F-type ATPase		Protein: 
F1Fo synthase, class 1
Find proteins for P00845 (Bacillus sp. (strain PS3))
Go to UniProtKB:  P00845
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP
Download SDF File 
Download CCD File 
A, B, C
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
PO4
Query on PO4
Download SDF File 
Download CCD File 
E
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ADP
Query on ADP
Download SDF File 
Download CCD File 
F
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG
Download SDF File 
Download CCD File 
A, B, C, F
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
b2
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

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 

  • Version 1.0: 2019-02-20
    Type: Initial release
  • Version 1.1: 2020-01-15
    Type: Author supporting evidence