3E9U

Crystal structure of Calx CBD2 domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.257 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of CBD2 from the Drosophila Na(+)/Ca(2+) exchanger: diversity of Ca(2+) regulation and its alternative splicing modification.

Wu, M.Wang, M.Nix, J.Hryshko, L.V.Zheng, L.

(2009) J.Mol.Biol. 387: 104-112

  • DOI: 10.1016/j.jmb.2009.01.045

  • PubMed Abstract: 
  • Na(+)/Ca(2+) exchangers (NCXs) promote the extrusion of intracellular Ca(2+) to terminate numerous Ca(2+)-mediated signaling processes. Ca(2+) interaction at two Ca(2+) binding domains (CBDs; CBD1 and CBD2) is important for tight regulation of the ex ...

    Na(+)/Ca(2+) exchangers (NCXs) promote the extrusion of intracellular Ca(2+) to terminate numerous Ca(2+)-mediated signaling processes. Ca(2+) interaction at two Ca(2+) binding domains (CBDs; CBD1 and CBD2) is important for tight regulation of the exchange activity. Diverse Ca(2+) regulatory properties have been reported with several NCX isoforms; whether the regulatory diversity of NCXs is related to structural differences of the pair of CBDs is presently unknown. Here, we reported the crystal structure of CBD2 from the Drosophila melanogaster exchanger CALX1.1. We show that the CALX1.1-CBD2 is an immunoglobulin-like structure, similar to mammalian NCX1-CBD2, but the predicted Ca(2+) interaction region of CALX1.1-CBD2 is arranged in a manner that precludes Ca(2+) binding. The carboxylate residues that coordinate two Ca(2+) in the NCX1-CBD1 structure are neutralized by two Lys residues in CALX1.1-CBD2. This structural observation was further confirmed by isothermal titration calorimetry. The CALX1.1-CBD2 structure also clearly shows the alternative splicing region forming two adjacent helices perpendicular to CBD2. Our results provide structural evidence that the diversity of Ca(2+) regulatory properties of NCX proteins can be achieved by (1) local structure rearrangement of Ca(2+) binding site to change Ca(2+) binding properties of CBD2 and (2) alternative splicing variation altering the protein domain-domain conformation to modulate the Ca(2+) regulatory behavior.


    Organizational Affiliation

    Center for Membrane Biology, Department of Biochemistry and Molecular Biology, the University of Texas Medical School at Houston, Houston, TX 77030, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Na/Ca exchange protein
A
162Drosophila melanogasterMutation(s): 0 
Gene Names: Calx (NCX)
Find proteins for Q24413 (Drosophila melanogaster)
Go to UniProtKB:  Q24413
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.257 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 113.365α = 90.00
b = 113.365β = 90.00
c = 41.616γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata scaling
REFMACrefinement
CrystalCleardata collection
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2008-08-23 
  • Released Date: 2009-01-27 
  • Deposition Author(s): Wu, M., Zheng, L.

Revision History 

  • Version 1.0: 2009-01-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance