3CGA | pdb_00003cga

Crystal structure of metastasis-associated protein S100A4 in the active, calcium-bound form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 
    0.331 (Depositor), 0.275 (DCC) 
  • R-Value Work: 
    0.268 (DCC) 
  • R-Value Observed: 
    0.255 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3CGA

This is version 1.2 of the entry. See complete history

Literature

Crystal structure of metastasis-associated protein S100A4 in the active calcium-bound form

Pathuri, P.Vogeley, L.Luecke, H.

(2008) J Mol Biology 383: 62-77

  • DOI: https://doi.org/10.1016/j.jmb.2008.04.076
  • Primary Citation Related Structures: 
    3CGA

  • PubMed Abstract: 

    S100A4 (metastasin) is a member of the S100 family of calcium-binding proteins that is directly involved in tumorigenesis. Until recently, the only structural information available was the solution NMR structure of the inactive calcium-free form of the protein. Here we report the crystal structure of human S100A4 in the active calcium-bound state at 2.03 A resolution that was solved by molecular replacement in the space group P6(5) with two molecules in the asymmetric unit from perfectly merohedrally twinned crystals. The Ca(2+)-bound S100A4 structure reveals a large conformational change in the three-dimensional structure of the dimeric S100A4 protein upon calcium binding. This calcium-dependent conformational change opens up a hydrophobic binding pocket that is capable of binding to target proteins such as annexin A2, the tumor-suppressor protein p53 and myosin IIA. The structure of the active form of S100A4 provides insight into its interactions with its binding partners and a better understanding of its role in metastasis.


  • Organizational Affiliation
    • Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA.

Macromolecule Content 

  • Total Structure Weight: 23.65 kDa 
  • Atom Count: 1,467 
  • Modeled Residue Count: 174 
  • Deposited Residue Count: 202 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Protein S100-A4
A, B
101Homo sapiensMutation(s): 0 
Gene Names: S100A4CAPLMTS1
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: 2.03 Å
  • R-Value Free:  0.331 (Depositor), 0.275 (DCC) 
  • R-Value Work:  0.268 (DCC) 
  • R-Value Observed: 0.255 (Depositor) 
Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.107α = 90
b = 47.107β = 90
c = 176.2γ = 120
Software Package:
Software NamePurpose
SHELXmodel building
SHELXL-97refinement
DENZOdata reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-09-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references, Derived calculations