4CFR

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.161 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1371/journal.pone.0097654
  • Primary Citation of Related Structures:  

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN S100-A4
A, B
104Homo sapiensMutation(s): 4 
Gene Names: S100A4 (CAPL, MTS1)
Find proteins for P26447 (Homo sapiens)
Go to Gene View: S100A4
Go to UniProtKB:  P26447
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
MYOSIN-9
Q
45Homo sapiensMutation(s): 1 
Gene Names: MYH9
Find proteins for P35579 (Homo sapiens)
Go to Gene View: MYH9
Go to UniProtKB:  P35579
Small Molecules
Ligands 1 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.161 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 64.140α = 90.00
b = 64.140β = 90.00
c = 138.220γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
CCP4phasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-05-07
    Type: Initial release
  • Version 1.1: 2014-05-28
    Type: Database references