2AGV

Crystal structure of the SR CA2+-ATPASE with BHQ and TG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.239 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Inaugural Article: Structural role of countertransport revealed in Ca2+ pump crystal structure in the absence of Ca2+.

Obara, K.Miyashita, N.Xu, C.Toyoshima, I.Sugita, Y.Inesi, G.Toyoshima, C.

(2005) Proc.Natl.Acad.Sci.USA 102: 14489-14496

  • DOI: 10.1073/pnas.0506222102
  • Also Cited By: 2ZBG, 2ZBF, 2ZBE, 2ZBD, 2Z9R, 2EAU, 2EAT, 2EAS, 2EAR, 2DQS

  • PubMed Abstract: 
  • Ca(2+)-ATPase of sarcoplasmic reticulum is an ATP-powered Ca(2+) pump but also a H(+) pump in the opposite direction with no demonstrated functional role. Here, we report a 2.4-A-resolution crystal structure of the Ca(2+)-ATPase in the absence of Ca( ...

    Ca(2+)-ATPase of sarcoplasmic reticulum is an ATP-powered Ca(2+) pump but also a H(+) pump in the opposite direction with no demonstrated functional role. Here, we report a 2.4-A-resolution crystal structure of the Ca(2+)-ATPase in the absence of Ca(2+) stabilized by two inhibitors, dibutyldihydroxybenzene, which bridges two transmembrane helices, and thapsigargin, also bound in the membrane region. Now visualized are water and several phospholipid molecules, one of which occupies a cleft between two transmembrane helices. Atomic models of the Ca(2+) binding sites with explicit hydrogens derived by continuum electrostatic calculations show how water and protons fill the space and compensate charge imbalance created by Ca(2+)-release. They suggest that H(+) countertransport is a consequence of a requirement for maintaining structural integrity of the empty Ca(2+)-binding sites. For this reason, cation countertransport is probably mandatory for all P-type ATPases and possibly accompanies transport of water as well.


    Related Citations: 
    • Crystal structure of the calcium pump of sarcoplasmic reticulum at 2.6 A resolution
      Toyoshima, C.,Nakasako, M.,Nomura, H.,Ogawa, H.
      (2000) Nature 405: 647
    • Lumenal gating mechanism revealed in calcium pump crystal structures with phosphate analogues
      Toyoshima, C.,Nomura, H.,Tsuda, T.
      (2004) Nature 432: 361
    • Structural changes in the calcium pump accompanying the dissociation of calcium
      Toyoshima, C.,Nomura, H.
      (2002) Nature 418: 605
    • Crystal structure of the calcium pump with a bound ATP analogue
      Toyoshima, C.,Mizutani, T.
      (2004) Nature 430: 529


    Organizational Affiliation

    Institute of Molecular and Cellular Biosciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Sarcoplasmic/endoplasmic reticulum calcium ATPase 1
A, B
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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BHQ
Query on BHQ

Download SDF File 
Download CCD File 
A, B
2,5-DITERT-BUTYLBENZENE-1,4-DIOL
2,5-DI-(TERT-BUTYL)-1,4,BENZOHYDROQUINONE
C14 H22 O2
JZODKRWQWUWGCD-UHFFFAOYSA-N
 Ligand Interaction
TG1
Query on TG1

Download SDF File 
Download CCD File 
A, B
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)OXY]-2-OXO-4-(1-OXOBUTOXY)-AZULENO[4,5-B]FURAN-7-YL ESTER
THAPSIGARGIN
C34 H50 O12
IXFPJGBNCFXKPI-FSIHEZPISA-N
 Ligand Interaction
NA
Query on NA

Download SDF File 
Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
PTY
Query on PTY

Download SDF File 
Download CCD File 
A, B
PHOSPHATIDYLETHANOLAMINE
C40 H80 N O8 P
NJGIRBISCGPRPF-KXQOOQHDSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
TG1Kd: 0.2 nM (100) BINDINGDB
TG1IC50: 0.2 nM (100) BINDINGDB
BHQKd: 20 nM BINDINGMOAD
BHQKd: 20 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.239 
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 71.385α = 90.00
b = 71.385β = 90.00
c = 591.017γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
CNSrefinement
CNSphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-10-25
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance