5A3Q | pdb_00005a3q

Crystal structure of the (SR) Calcium ATPase E2-vanadate complex bound to thapsigargin and TNP-AMPPCP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 
    0.258 (Depositor), 0.269 (DCC) 
  • R-Value Work: 
    0.200 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 
    0.203 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.0 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.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 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.

Macromolecule Content 

  • Total Structure Weight: 111.22 kDa 
  • Atom Count: 7,775 
  • Modeled Residue Count: 995 
  • Deposited Residue Count: 995 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
SARCOPLASMIC/ENDOPLASMIC RETICULUM CALCIUM ATPASE 1995Oryctolagus cuniculusMutation(s): 1 
EC: 3.6.3.8 (PDB Primary Data), 7.2.2.10 (UniProt)
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
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Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DL5

Query on DL5



Download:Ideal Coordinates CCD File
D [auth A]Spiro(2,4,6-trinitrobenzene[1,2a]-O2',O3'-methylene-adenosine (beta,gamma-methylene)triphosphate
C17 H18 N8 O18 P3
IPYWFNMUWLRGLC-KWDXPJCYSA-N
TG1

Query on TG1



Download:Ideal Coordinates CCD File
B [auth A]OCTANOIC ACID [3S-[3ALPHA, 3ABETA, 4ALPHA, 6BETA, 6ABETA, 7BETA, 8ALPHA(Z), 9BALPHA]]-6-(ACETYLOXY)-2,3,-3A,4,5,6,6A,7,8,9B-DECAHYDRO-3,3A-DIHYDROXY-3,6,9-TRIMETHYL-8-[(2-METHYL-1-OXO-2-BUTENYL)OX Y]-2-OXO-4-(1-OXOBUTOXY)-AZULENO[4,5-B]FURAN-7-YL ESTER
C34 H50 O12
IXFPJGBNCFXKPI-FSIHEZPISA-N
VN4

Query on VN4



Download:Ideal Coordinates CCD File
C [auth A]oxido(dioxo)vanadium
O3 V
ALTWGIIQPLQAAM-UHFFFAOYSA-N
K

Query on K



Download:Ideal Coordinates CCD File
G [auth A]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
H [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG

Query on MG



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free:  0.258 (Depositor), 0.269 (DCC) 
  • R-Value Work:  0.200 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 0.203 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.427α = 90
b = 118.781β = 90
c = 141.828γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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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: 2018-03-07
    Changes: Data collection
  • Version 1.3: 2019-05-15
    Changes: Data collection, Derived calculations, Experimental preparation
  • Version 1.4: 2019-10-23
    Changes: Data collection, Database references, Other
  • Version 1.5: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 1.6: 2024-11-06
    Changes: Structure summary
  • Version 2.0: 2026-04-15
    Changes: Data collection, Non-polymer description, Structure summary