7DQC

Crystal structure of nucleotide-free mutant A(S23C)3B(N64C)3 complex from Enterococcus hirae V-ATPase

• PDB DOI: https://doi.org/10.2210/pdb7DQC/pdb

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


• Deposited: 2020-12-23 Released: 2021-12-29 
• Deposition Author(s): Maruyama, S., Suzuki, K., Mizutani, K., Imai, F.L., Ishizuka-Katsura, Y., Shirouzu, M., Murata, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.71 Å
• R-Value Free: 
  0.266 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.234 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.236 (Depositor) 

Starting Model: experimental

Literature

The combination of high-speed AFM and X-ray crystallography reveals rotary catalytic mechanism of shaftless V1-ATPase

Imamura, M., Maruyama, S., Nakamoto, K., Kawai, F., Akiyama, T., Mizutani, K., Suzuki, K., Shirouzu, M., Iino, R., Uchihashi, T., Ando, T., Murata, T.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A3B3 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 6-mer - A5B1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 354.77 kDa 
• Atom Count: 23,812 
• Modelled Residue Count: 3,104 
• Deposited Residue Count: 3,195 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type sodium ATPase catalytic subunit A	A, B, E [auth C]	600	Enterococcus hirae ATCC 9790	Mutation(s): 1  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	C [auth D], D [auth E], F	465	Enterococcus hirae ATCC 9790	Mutation(s): 1  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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.71 Å
• R-Value Free:  0.266 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.234 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.236 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.08	α = 90
b = 121.83	β = 90.22
c = 129.11	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-12-29 
Deposition Author(s): Maruyama, S., Suzuki, K., Mizutani, K., Imai, F.L., Ishizuka-Katsura, Y., Shirouzu, M., Murata, M.

Revision History  

• Version 1.0: 2021-12-29
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary