Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction | Predict Membrane 

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 22-mer - A10B3C3D2E1F1G1H1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 22-mer - A10B6C1D1E1F1G1H1 

Local Symmetry: Cyclic - C10  (3D View)
Local Stoichiometry: Homo 10-mer - A10 Local Symmetry: Cyclic - C3  (3D View)
Local Stoichiometry: Hetero 6-mer - B3C3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: microscopy

Macromolecule Content

• Total Structure Weight: 526.60 kDa 
• Atom Count: 35043 
• Modelled Residue Count: 4713 
• Deposited Residue Count: 4814 
• Unique protein chains: 9

6N2Y

Bacillus PS3 ATP synthase class 1

• PDB DOI: 10.2210/pdb6N2Y/pdb
• EM Map EMD-9333:EMDBEMDataResource

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


• 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)

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Experimental Data Snapshot

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

Literature

Structure of a bacterial ATP synthase.

Guo, H., Suzuki, T., Rubinstein, J.L.

(2019) Elife 8

• PubMed: 30724163 
• DOI: 10.7554/eLife.43128
• Primary Citation of 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit alpha	A, B, C	502	Bacillus sp. PS3	Mutation(s): 0  Gene Names: uncA, atpA 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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit beta	D, E, F	473	Bacillus sp. PS3	Mutation(s): 0  Gene Names: uncD, atpD 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 ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase gamma chain	G	285	Bacillus sp. PS3	Mutation(s): 0  Gene Names: uncG, atpG Membrane Entity: Yes
UniProt
Find proteins for A0A0M4TPJ7 (Bacillus sp. (strain PS3)) Explore A0A0M4TPJ7  Go to UniProtKB:  A0A0M4TPJ7

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase epsilon chain	H	133	Bacillus sp. PS3	Mutation(s): 0  Gene Names: uncC, atpC Membrane Entity: Yes
UniProt
Find proteins for A0A0M5MQR7 (Bacillus sp. (strain PS3)) Explore A0A0M5MQR7  Go to UniProtKB:  A0A0M5MQR7

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit delta	I	178	Bacillus sp. PS3	Mutation(s): 0

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit b	J [auth b2]	168	Bacillus sp. PS3	Mutation(s): 0

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit b	K [auth b1]	168	Bacillus sp. PS3	Mutation(s): 0

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit a	L [auth a]	237	Bacillus sp. PS3	Mutation(s): 0

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit c	M [auth c0], N [auth c1], O [auth c2], P [auth c3], Q [auth c4], R [auth c5], S [auth c6], T [auth c7], U [auth c8], V [auth c9]	72	Bacillus sp. PS3	Mutation(s): 0  Gene Names: atpE, uncE Membrane Entity: Yes
UniProt
Find proteins for P00845 (Bacillus sp. (strain PS3)) Explore P00845  Go to UniProtKB:  P00845

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	AA [auth C], W [auth A], Y [auth B]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP	DA [auth F]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
PO4	CA [auth E]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
MG	BA [auth C], EA [auth F], X [auth A], Z [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-11-14 
• Released Date: 2019-02-20 
Deposition Author(s): Guo, H., Rubinstein, J.L.

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Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	MOP 81294
Japan Society for the Promotion of Science (JSPS)	Japan	JP18H02409

Revision History  

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