3RRK | pdb_00003rrk

Crystal structure of the cytoplasmic N-terminal domain of subunit I, homolog of subunit a, of V-ATPase

• PDB DOI: https://doi.org/10.2210/pdb3RRK/pdb

• Classification: PROTON TRANSPORT
• Organism(s): Meiothermus ruber DSM 1279
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-04-29 Released: 2011-08-10 
• Deposition Author(s): Srinivasan, S., Vyas, N.K., Baker, M.L., Quiocho, F.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.64 Å
• R-Value Free: 
  0.255 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the cytoplasmic N-terminal domain of subunit I, a homolog of subunit a, of V-ATPase.

Srinivasan, S., Vyas, N.K., Baker, M.L., Quiocho, F.A.

(2011) J Mol Biology 412: 14-21

• PubMed: 21787787 
• DOI: https://doi.org/10.1016/j.jmb.2011.07.014
• Primary Citation Related Structures: 
  3RRK


• PubMed Abstract: 
  

  Subunit "a" is associated with the membrane-bound (V(O)) complex of eukaryotic vacuolar H(+)-ATPase acidification machinery. It has also been shown recently to be involved in diverse membrane fusion/secretory functions independent of acidification. Here, we report the crystal structure of the N-terminal cytosolic domain from the Meiothermus ruber subunit "I" homolog of subunit a. The structure is composed of a curved long central α-helix bundle capped on both ends by two lobes with similar α/β architecture. Based on the structure, a reasonable model of its eukaryotic subunit a counterpart was obtained. The crystal structure and model fit well into reconstructions from electron microscopy of prokaryotic and eukaryotic vacuolar H(+)-ATPases, respectively, clarifying their orientations and interactions and revealing features that could enable subunit a to play a role in membrane fusion/secretion.

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Organizational Affiliation: 
• Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 39.41 kDa 
• Atom Count: 2,384 
• Modeled Residue Count: 301 
• Deposited Residue Count: 357 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
V-type ATPase 116 kDa subunit	A	357	Meiothermus ruber DSM 1279	Mutation(s): 0  Gene Names: Mrub_0956
UniProt
Find proteins for D3PQI8 (Meiothermus ruber (strain ATCC 35948 / DSM 1279 / VKM B-1258 / 21)) Explore D3PQI8  Go to UniProtKB:  D3PQI8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NHE	B [auth A], C [auth A]	2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID C8 H17 N O3 S MKWKNSIESPFAQN-UHFFFAOYSA-N
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.64 Å
• R-Value Free:  0.255 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.32	α = 90
b = 102.181	β = 90
c = 139.062	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
PHENIX	model building
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-08-10 
Deposition Author(s): Srinivasan, S., Vyas, N.K., Baker, M.L., Quiocho, F.A.

Revision History  

• Version 1.0: 2011-08-10
  Type: Initial release
  
• Version 1.1: 2011-11-30
  Changes: Database references
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations
• Version 1.3: 2024-04-03
  Changes: Refinement description