5A3R

Crystal structure of the (SR) Calcium ATPase E2.BeF3- complex bound to TNP-AMPPCP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Crystal Structure of the Vanadate-Inhibited Ca(2+)-ATPase.

Clausen, J.D.Bublitz, M.Arnou, B.Olesen, C.Andersen, J.P.Moller, J.V.Nissen, P.

(2016) Structure 24: 617

  • DOI: https://doi.org/10.1016/j.str.2016.02.018
  • Primary Citation of Related Structures:  
    5A3Q, 5A3R, 5A3S

  • PubMed Abstract: 

    Vanadate is the hallmark inhibitor of the P-type ATPase family; however, structural details of its inhibitory mechanism have remained unresolved. We have determined the crystal structure of sarcoplasmic reticulum Ca(2+)-ATPase with bound vanadate in the absence of Ca(2+). Vanadate is bound at the catalytic site as a planar VO3(-) in complex with water and Mg(2+) in a dephosphorylation transition-state-like conformation. Validating bound VO3(-) by anomalous difference Fourier maps using long-wavelength data we also identify a hitherto undescribed Cl(-) site near the dephosphorylation site. Crystallization was facilitated by trinitrophenyl (TNP)-derivatized nucleotides that bind with the TNP moiety occupying the binding pocket that normally accommodates the adenine of ATP, rationalizing their remarkably high affinity for E2P-like conformations of the Ca(2+)-ATPase. A comparison of the configurations of bound nucleotide analogs in the E2·VO3(-) structure with that in E2·BeF3(-) (E2P ground state analog) reveals multiple binding modes to the Ca(2+)-ATPase.


  • Organizational Affiliation

    Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark; Centre for Membrane Pumps in Cells and Disease - PUMPKIN, Danish National Research Foundation, Aarhus University, 8000 Aarhus, Denmark; Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SARCOPLASMIC/ENDOPLASMIC RETICULUM CALCIUM ATPASE 1994Oryctolagus cuniculusMutation(s): 0 
EC: 3.6.3.8
Membrane Entity: Yes 
UniProt
Find proteins for P04191 (Oryctolagus cuniculus)
Explore P04191 
Go to UniProtKB:  P04191
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04191
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
BFD
Query on BFD
A
L-PEPTIDE LINKINGC4 H6 Be F3 N O4ASP
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.53α = 90
b = 114.967β = 90
c = 227.699γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-04-13
    Type: Initial release
  • Version 1.1: 2016-04-20
    Changes: Database references
  • Version 1.2: 2019-05-15
    Changes: Data collection, Derived calculations, Experimental preparation, Other
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description