3C1V | pdb_00003c1v

The 1.5 A Crystal structure of Ca2+-bound S100A4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.218 (Depositor), 0.215 (DCC) 
  • R-Value Work: 
    0.195 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 
    0.196 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 3C1V

This is version 1.3 of the entry. See complete history

Literature

Crystal structure of the Ca(2+)-form and Ca(2+)-binding kinetics of metastasis-associated protein, S100A4

Gingras, A.R.Basran, J.Prescott, A.Kriajevska, M.Bagshaw, C.R.Barsukov, I.L.

(2008) FEBS Lett 582: 1651-1656

  • DOI: https://doi.org/10.1016/j.febslet.2008.04.017
  • Primary Citation Related Structures: 
    3C1V

  • PubMed Abstract: 

    S100A4 takes part in control of tumour cell migration and contributes to metastatic spread in in vivo models. In the active dimeric Ca(2+)-bound state it interacts with multiple intracellular targets. Conversely, oligomeric forms of S100A4 are linked with the extracellular function of this protein. We report the 1.5A X-ray crystal structure of Ca(2+)-bound S100A4 and use it to identify the residues involved in target recognition and to derive a model of the oligomeric state. We applied stopped-flow analysis of tyrosine fluorescence to derive kinetics of S100A4 activation by Ca(2+) (k(on)=3.5 microM(-1)s(-1), k(off)=20s(-1)).


  • Organizational Affiliation
    • Department of Biochemistry, University of Leicester, Henry Wellcome Building, Leicester LE1 9HN, UK.

Macromolecule Content 

  • Total Structure Weight: 52.92 kDa 
  • Atom Count: 3,814 
  • Modeled Residue Count: 380 
  • Deposited Residue Count: 452 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein S100-A4
A, B, C, D
113Homo sapiensMutation(s): 0 
Gene Names: S100A4
UniProt & NIH Common Fund Data Resources
Find proteins for P26447 (Homo sapiens)
Explore P26447 
Go to UniProtKB:  P26447
PHAROS:  P26447
GTEx:  ENSG00000196154 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP26447
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free:  0.218 (Depositor), 0.215 (DCC) 
  • R-Value Work:  0.195 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 0.196 (Depositor) 
Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.32α = 90
b = 52.32β = 90
c = 139.14γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MxCuBEdata collection
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-04-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2018-01-31
    Changes: Experimental preparation
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description