1SU4

Crystal structure of calcium ATPase with two bound calcium ions


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.246 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

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: 647-655

  • DOI: 10.1038/35015017
  • Primary Citation of Related Structures:  
    1SU4

  • PubMed Abstract: 
  • Calcium ATPase is a member of the P-type ATPases that transport ions across the membrane against a concentration gradient. Here we have solved the crystal structure of the calcium ATPase of skeletal muscle sarcoplasmic reticulum (SERCA1a) at 2.6 A resolution with two calcium ions bound in the transmembrane domain, which comprises ten alpha-helices ...

    Calcium ATPase is a member of the P-type ATPases that transport ions across the membrane against a concentration gradient. Here we have solved the crystal structure of the calcium ATPase of skeletal muscle sarcoplasmic reticulum (SERCA1a) at 2.6 A resolution with two calcium ions bound in the transmembrane domain, which comprises ten alpha-helices. The two calcium ions are located side by side and are surrounded by four transmembrane helices, two of which are unwound for efficient coordination geometry. The cytoplasmic region consists of three well separated domains, with the phosphorylation site in the central catalytic domain and the adenosine-binding site on another domain. The phosphorylation domain has the same fold as haloacid dehalogenase. Comparison with a low-resolution electron density map of the enzyme in the absence of calcium and with biochemical data suggests that large domain movements take place during active transport.


    Related Citations: 
    • Structural changes in the calcium pump accompanying the dissociation of calcium.
      Toyoshima, C., Nomura, H.
      (2002) Nature 418: 605
    • Structural basis of ion pumping by Ca(2+)-ATPase of sarcoplasmic reticulum.
      Toyoshima, C., Nomura, H., Sugita, Y.
      (2003) FEBS Lett 555: 106

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Sarcoplasmic/endoplasmic reticulum calcium ATPase 1A994Oryctolagus cuniculusMutation(s): 0 
Gene Names: ATP2A1
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download Ideal Coordinates CCD File 
B [auth A], C [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
D [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.246 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 165.89α = 90
b = 64.34β = 98.08
c = 147.14γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
MLPHAREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-05-04
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2013-05-22
    Changes: Database references
  • Version 1.4: 2017-10-11
    Changes: Refinement description