7COQ | pdb_00007coq

Hexameric Ring Complex of Engineered V1-ATPase bound to AMP-PNP: A3(De)3_(ANP)1cat

• PDB DOI: https://doi.org/10.2210/pdb7COQ/pdb

• Classification: MOTOR PROTEIN
• Organism(s): Enterococcus hirae ATCC 9790
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2020-08-05 Released: 2021-08-11 
• Deposition Author(s): Kosugi, T., Tanabe, M., Koga, N.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Agency for Medical Research and Development (AMED), Japan Science and Technology

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.44 Å
• R-Value Free: 
  0.248 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.213 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.214 (Depositor) 

Starting Model: experimental

Literature

De Novo Design of Allosteric Control into Rotary Motor V1-ATPase by Restoring Lost Function

Kosugi, T., Iida, T., Tanabe, M., Iino, R., Koga, N.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A3B3 Pseudo Symmetry: Cyclic - C6  (Explore in 3D)
Pseudo Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 351.76 kDa 
• Atom Count: 24,060 
• Modeled Residue Count: 3,082 
• Deposited Residue Count: 3,162 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type sodium ATPase catalytic subunit A	A, B, C	596	Enterococcus hirae ATCC 9790	Mutation(s): 0  Gene Names: ntpA, EHR_08260 EC: 7.2.2.1
UniProt
Find proteins for Q08636 (Enterococcus hirae (strain ATCC 9790 / DSM 20160 / JCM 8729 / LMG 6399 / NBRC 3181 / NCIMB 6459 / NCDO 1258 / NCTC 12367 / WDCM 00089 / R)) Explore Q08636  Go to UniProtKB:  Q08636

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type sodium ATPase subunit B	D, E, F	458	Enterococcus hirae ATCC 9790	Mutation(s): 10  Gene Names: ntpB, EHR_08265
UniProt
Find proteins for Q08637 (Enterococcus hirae (strain ATCC 9790 / DSM 20160 / JCM 8729 / LMG 6399 / NBRC 3181 / NCIMB 6459 / NCDO 1258 / NCTC 12367 / WDCM 00089 / R)) Explore Q08637  Go to UniProtKB:  Q08637

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP (Subject of Investigation/LOI)	H [auth C]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N
MG (Subject of Investigation/LOI)	G [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.44 Å
• R-Value Free:  0.248 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.213 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.445	α = 90
b = 124.486	β = 93.03
c = 131.339	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data processing
Aimless	data scaling
PHASER	phasing
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-08-11 
Deposition Author(s): Kosugi, T., Tanabe, M., Koga, N.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	18H05420
Japan Agency for Medical Research and Development (AMED)	Japan	JP20am0101071
Japan Science and Technology	Japan	JPMJPR13AD

Revision History  

• Version 1.0: 2021-08-11
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description