4DUQ

The Structure of Ca2+-loaded S100A2 at 1.3A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.136 
  • R-Value Observed: 0.138 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The structure of Ca2+-loaded S100A2 at 1.3- angstrom resolution.

Koch, M.Fritz, G.

(2012) FEBS J 279: 1799-1810

  • DOI: https://doi.org/10.1111/j.1742-4658.2012.08556.x
  • Primary Citation of Related Structures:  
    4DUQ

  • PubMed Abstract: 

    S100A2 is an EF-hand calcium ion (Ca(2+))-binding protein that activates the tumour suppressor p53. In order to understand the molecular mechanisms underlying the Ca(2+) -induced activation of S100A2, the structure of Ca(2+)-bound S100A2 was determined at 1.3 Å resolution by X-ray crystallography. The structure was compared with Ca(2+) -free S100A2 and with other S100 proteins. Binding of Ca(2+) to S100A2 induces small structural changes in the N-terminal EF-hand, but a large conformational change in the C-terminal EF-hand, reorienting helix III by approximately 90°. This movement is accompanied by the exposure of a hydrophobic cavity between helix III and helix IV that represents the target protein interaction site. This molecular reorganization is associated with the breaking and new formation of intramolecular hydrophobic contacts. The target binding site exhibits unique features; in particular, the hydrophobic cavity is larger than in other Ca(2+)-loaded S100 proteins. The structural data underline that the shape and size of the hydrophobic cavity are major determinants for target specificity of S100 proteins and suggest that the binding mode for S100A2 is different from that of other p53-interacting S100 proteins. Database Structural data are available in the Protein Data Bank database under the accession number 4DUQ


  • Organizational Affiliation

    Bayer Schering Pharma AG, Wuppertal, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein S100-A2
A, B
98Homo sapiensMutation(s): 3 
Gene Names: S100A2S100L
UniProt & NIH Common Fund Data Resources
Find proteins for P29034 (Homo sapiens)
Explore P29034 
Go to UniProtKB:  P29034
PHAROS:  P29034
GTEx:  ENSG00000196754 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29034
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.136 
  • R-Value Observed: 0.138 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.67α = 90
b = 84.67β = 90
c = 58.3γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
SHELXphasing
REFMACrefinement
PDB_EXTRACTdata extraction
SHELXDphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-03-07
    Type: Initial release
  • Version 1.1: 2012-03-28
    Changes: Database references
  • Version 1.2: 2014-03-12
    Changes: Database references
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references, Derived calculations