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 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1016/j.str.2016.02.018
  • Primary Citation of Related Structures:  

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SARCOPLASMIC/ENDOPLASMIC RETICULUM CALCIUM ATPASE 1
A
994Oryctolagus cuniculusMutation(s): 0 
Gene Names: ATP2A1
EC: 7.2.2.10
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
P-type ATPase
Protein: 
Calcium ATPase; rabbit sarcoplasmic reticulum. E1 state with bound calcium
Find proteins for P04191 (Oryctolagus cuniculus)
Go to Gene View: ATP2A1
Go to UniProtKB:  P04191
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
DL5
Query on DL5

Download SDF File 
Download CCD File 
A
Spiro(2,4,6-trinitrobenzene[1,2a]-O2',O3'-methylene-adenosine (beta,gamma-methylene)triphosphate
TNP-AMPPCP
C17 H19 N8 O18 P3
WOUJMFLAWZHYLK-KWDXPJCYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D 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 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 57.530α = 90.00
b = 114.967β = 90.00
c = 227.699γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-04-13
    Type: Initial release
  • Version 1.1: 2016-04-20
    Type: Database references