4DUQ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.136 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1111/j.1742-4658.2012.08556.x

  • 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 determin ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein S100-A2
A, B
98Homo sapiensMutation(s): 3 
Gene Names: S100A2 (S100L)
Find proteins for P29034 (Homo sapiens)
Go to Gene View: S100A2
Go to UniProtKB:  P29034
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
15P
Query on 15P

Download SDF File 
Download CCD File 
B
POLYETHYLENE GLYCOL (N=34)
PEG 1500
C69 H140 O35
VUYXVWGKCKTUMF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.136 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 84.670α = 90.00
b = 84.670β = 90.00
c = 58.300γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
SHELXDphasing
SHELXphasing
PDB_EXTRACTdata extraction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-02-22 
  • Released Date: 2012-03-07 
  • Deposition Author(s): Koch, M., Fritz, G.
  • This entry supersedes: 3N22

Revision History 

  • Version 1.0: 2012-03-07
    Type: Initial release
  • Version 1.1: 2012-03-28
    Type: Database references
  • Version 1.2: 2014-03-12
    Type: Database references