5A1M

Crystal structure of calcium-bound human adseverin domain A3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Calcium-Controlled Conformational Choreography in the N-Terminal Half of Adseverin.

Chumnarnsilpa, S.Robinson, R.C.Grimes, J.M.Leyrat, C.

(2015) Nat.Commun. 6: 8254

  • DOI: 10.1038/ncomms9254
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Adseverin is a member of the calcium-regulated gelsolin superfamily of actin-binding proteins. Here we report the crystal structure of the calcium-free N-terminal half of adseverin (iA1-A3) and the Ca(2+)-bound structure of A3, which reveal structura ...

    Adseverin is a member of the calcium-regulated gelsolin superfamily of actin-binding proteins. Here we report the crystal structure of the calcium-free N-terminal half of adseverin (iA1-A3) and the Ca(2+)-bound structure of A3, which reveal structural similarities and differences with gelsolin. Solution small-angle X-ray scattering combined with ensemble optimization revealed a dynamic Ca(2+)-dependent equilibrium between inactive, intermediate and active conformations. Increasing calcium concentrations progressively shift this equilibrium from a main population of inactive conformation to the active form. Molecular dynamics simulations of iA1-A3 provided insights into Ca(2+)-induced destabilization, implicating a critical role for the A2 type II calcium-binding site and the A2A3 linker in the activation process. Finally, mutations that disrupt the A1/A3 interface increase Ca(2+)-independent F-actin severing by A1-A3, albeit at a lower efficiency than observed for gelsolin domains G1-G3. Together, these data address the calcium dependency of A1-A3 activity in relation to the calcium-independent activity of G1-G3.


    Organizational Affiliation

    Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138673, Singapore.,Department of Biochemistry, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore.,Science Division, Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE, UK.,Division of Structural Biology, University of Oxford, Henry Wellcome Building for Genomic Medicine, Oxford OX3 7BN, UK.,School of Biochemistry, Institute of Science, Suranaree University of Technology, 111 University Avenue, Muang, Nakhon Ratchasima 30000, Thailand.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ADSEVERIN
A
104Homo sapiensMutation(s): 0 
Gene Names: SCIN (KIAA1905)
Find proteins for Q9Y6U3 (Homo sapiens)
Go to Gene View: SCIN
Go to UniProtKB:  Q9Y6U3
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.182 
  • Space Group: I 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 92.510α = 90.00
b = 92.510β = 90.00
c = 68.910γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
SCALAdata scaling
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-09-16
    Type: Initial release
  • Version 1.1: 2015-09-23
    Type: Database references