8HH2

F1 domain of FoF1-ATPase from Bacillus PS3,post-hyd,highATP

• PDB DOI: https://doi.org/10.2210/pdb8HH2/pdb
• EM Map EMD-34749: EMDB EMDataResource

• Classification: MOTOR PROTEIN
• Organism(s): Bacillus sp. PS3
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2022-11-16 Released: 2023-07-19 
• Deposition Author(s): Nakano, A., Kishikawa, J., Mitsuoka, K., Yokoyama, K.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Agency for Medical Research and Development (AMED)

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Experimental Data Snapshot

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

Starting Model: experimental

Literature

Rotation mechanism of ATP synthases driven by ATP hydrolysis

Nakano, A., Yokoyama, K., Kishikawa, J., Mitsuoka, K.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 7-mer - A3B3C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 7-mer - A6B1 Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Hetero 6-mer - A3B3 

Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Hetero 6-mer - A3B3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 359.43 kDa 
• Atom Count: 24,281 
• Modelled Residue Count: 3,129 
• Deposited Residue Count: 3,239 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase subunit alpha	A, B, C	501	Bacillus sp. PS3	Mutation(s): 0  Gene Names: uncA, atpA EC: 7.1.2.2
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	484	Bacillus sp. PS3	Mutation(s): 0  Gene Names: uncD, atpD EC: 7.1.2.2
UniProt
Find proteins for P07677 (Bacillus sp. (strain PS3)) Explore P07677  Go to UniProtKB:  P07677

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP synthase gamma chain	G	284	Bacillus sp. PS3	Mutation(s): 0  Gene Names: uncG, atpG
UniProt
Find proteins for A0A0M4TPJ7 (Bacillus sp. (strain PS3)) Explore A0A0M4TPJ7  Go to UniProtKB:  A0A0M4TPJ7

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP (Subject of Investigation/LOI)	H [auth A], J [auth B], M [auth C], Q [auth E], T [auth F]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP (Subject of Investigation/LOI)	P [auth D]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
PO4 (Subject of Investigation/LOI)	N [auth D], R [auth E]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
MG (Subject of Investigation/LOI)	I [auth A], K [auth B], L [auth C], O [auth D], S [auth F]	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 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	RELION	4.0

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-07-19 
Deposition Author(s): Nakano, A., Kishikawa, J., Mitsuoka, K., Yokoyama, K.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	20H03231
Japan Society for the Promotion of Science (JSPS)	Japan	20K06514
Japan Agency for Medical Research and Development (AMED)	Japan	JP17am0101001
Japan Society for the Promotion of Science (JSPS)	Japan	20J00162

Revision History  

• Version 1.0: 2023-07-19
  Type: Initial release
  
• Version 1.1: 2024-07-03
  Changes: Data collection, Refinement description