6N2Y

Bacillus PS3 ATP synthase class 1

  • Classification: HYDROLASE
  • Organism(s): Bacillus sp. PS3
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2018-11-14 Released: 2019-02-20 
  • Deposition Author(s): Guo, H., Rubinstein, J.L.
  • Funding Organization(s): Canadian Institutes of Health Research (CIHR), Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 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:  
    6N2Z, 6N2Y, 6N30, 6N2D

  • 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 Biochemistry, The University of Toronto, Toronto, Canada.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase subunit alphaABC502Bacillus sp. PS3Mutation(s): 0 
Gene Names: uncAatpA
EC: 3.6.3.14 (PDB Primary Data), 7.1.2.2 (UniProt)
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))
Explore A0A0M3VGF9 
Go to UniProtKB:  A0A0M3VGF9
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase subunit betaDEF473Bacillus sp. PS3Mutation(s): 0 
Gene Names: uncDatpD
EC: 3.6.3.14 (PDB Primary Data), 7.1.2.2 (UniProt)
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))
Explore A0A0M4U1P9 
Go to UniProtKB:  A0A0M4U1P9
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase gamma chainG285Bacillus sp. PS3Mutation(s): 0 
Gene Names: uncGatpG
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))
Explore A0A0M4TPJ7 
Go to UniProtKB:  A0A0M4TPJ7
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase epsilon chainH133Bacillus sp. PS3Mutation(s): 0 
Gene Names: uncCatpC
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))
Explore A0A0M5MQR7 
Go to UniProtKB:  A0A0M5MQR7
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase subunit deltaI178Bacillus sp. PS3Mutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase subunit bb2168Bacillus sp. PS3Mutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase subunit bb1168Bacillus sp. PS3Mutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase subunit aa237Bacillus sp. PS3Mutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
ATP synthase subunit cc0c1c2c3c4c5c6c7c8c972Bacillus sp. PS3Mutation(s): 0 
Gene Names: atpEuncE
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))
Explore P00845 
Go to UniProtKB:  P00845
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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 
F
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
PO4
Query on PO4

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

Download CCD File 
A, B, C, F
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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 

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