1IWO

Crystal structure of the SR Ca2+-ATPase in the absence of Ca2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.237 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural changes in the calcium pump accompanying the dissociation of calcium

Toyoshima, C.Nomura, H.

(2002) Nature 418: 605-611

  • DOI: 10.1038/nature00944
  • Also Cited By: 2ZBG, 2ZBF, 2ZBE, 2ZBD, 2Z9R, 2EAU, 2EAT, 2EAS, 2EAR, 2DQS

  • PubMed Abstract: 
  • In skeletal muscle, calcium ions are transported (pumped) against a concentration gradient from the cytoplasm into the sarcoplasmic reticulum, an intracellular organelle. This causes muscle cells to relax after cytosolic calcium increases during exci ...

    In skeletal muscle, calcium ions are transported (pumped) against a concentration gradient from the cytoplasm into the sarcoplasmic reticulum, an intracellular organelle. This causes muscle cells to relax after cytosolic calcium increases during excitation. The Ca(2+) ATPase that carries out this pumping is a representative P-type ion-transporting ATPase. Here we describe the structure of this ion pump at 3.1 A resolution in a Ca(2+)-free (E2) state, and compare it with that determined previously for the Ca(2+)-bound (E1Ca(2+)) state. The structure of the enzyme stabilized by thapsigargin, a potent inhibitor, shows large conformation differences from that in E1Ca(2+). Three cytoplasmic domains gather to form a single headpiece, and six of the ten transmembrane helices exhibit large-scale rearrangements. These rearrangements ensure the release of calcium ions into the lumen of sarcoplasmic reticulum and, on the cytoplasmic side, create a pathway for entry of new calcium ions.


    Related Citations: 
    • The crystal and molecular structure of the sesquiterpenoid silerin (trilobolide)
      Kutschabsky, L.,Kretschmer, R.-G.,Ripperger, H.
      (1986) Cryst.Res.Technol. 21: 627
    • 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
    • Sesquiterpenoids from Thapsia species and medicinal chemistry of the thapsigargins
      Christensen, S.B.,Andersen, A.,Smitt, U.W.
      (1997) Fortschr.Chem.Org.Naturst. 71: 129


    Organizational Affiliation

    Institute of Molecular and Cellular Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan. ct@iam.u-tokyo.ac.jp




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Sarcoplasmic/endoplasmic reticulum calcium ATPase 1
A, B
994Oryctolagus cuniculusGene Names: ATP2A1
EC: 3.6.3.8
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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
TG1Kd: 0.2 nM (100) BINDINGDB
TG1IC50: 0.2 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.237 
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 71.739α = 90.00
b = 71.739β = 90.00
c = 590.300γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
X-PLORphasing
SCALEPACKdata scaling
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-08-14
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance