4CFR

Ca-bound S100A4 C3S, C81S, C86S and F45W mutant complexed with non- muscle myosin IIA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.161 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

The C-Terminal Random Coil Region Tunes the Ca2+-Binding Affinity of S100A4 Through Conformational Activation.

Duelli, A.Kiss, B.Lundholm, I.Bodor, A.Radnai, L.Petoukhov, M.Svergun, D.Nyitray, L.Katona, G.

(2014) PLoS One 9: 97654

  • DOI: https://doi.org/10.1371/journal.pone.0097654
  • Primary Citation of Related Structures:  
    4CFQ, 4CFR

  • PubMed Abstract: 

    S100A4 interacts with many binding partners upon Ca2+ activation and is strongly associated with increased metastasis formation. In order to understand the role of the C-terminal random coil for the protein function we examined how small angle X-ray scattering of the wild-type S100A4 and its C-terminal deletion mutant (residues 1-88, Δ13) changes upon Ca2+ binding. We found that the scattering intensity of wild-type S100A4 changes substantially in the 0.15-0.25 Å-1 q-range whereas a similar change is not visible in the C-terminus deleted mutant. Ensemble optimization SAXS modeling indicates that the entire C-terminus is extended when Ca2+ is bound. Pulsed field gradient NMR measurements provide further support as the hydrodynamic radius in the wild-type protein increases upon Ca2+ binding while the radius of Δ13 mutant does not change. Molecular dynamics simulations provide a rational explanation of the structural transition: the positively charged C-terminal residues associate with the negatively charged residues of the Ca2+-free EF-hands and these interactions loosen up considerably upon Ca2+-binding. As a consequence the Δ13 mutant has increased Ca2+ affinity and is constantly loaded at Ca2+ concentration ranges typically present in cells. The activation of the entire C-terminal random coil may play a role in mediating interaction with selected partner proteins of S100A4.


  • Organizational Affiliation

    Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN S100-A4
A, B
104Homo sapiensMutation(s): 4 
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
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
MYOSIN-9C [auth Q]45Homo sapiensMutation(s): 1 
UniProt & NIH Common Fund Data Resources
Find proteins for P35579 (Homo sapiens)
Explore P35579 
Go to UniProtKB:  P35579
PHAROS:  P35579
GTEx:  ENSG00000100345 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35579
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.161 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.14α = 90
b = 64.14β = 90
c = 138.22γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALEPACKdata scaling
CCP4phasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-05-07
    Type: Initial release
  • Version 1.1: 2014-05-28
    Changes: Database references
  • Version 2.0: 2019-10-23
    Changes: Advisory, Atomic model, Data collection, Other
  • Version 2.1: 2023-12-20
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description