3E9U

Crystal structure of Calx CBD2 domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.257 
  • R-Value Observed: 0.258 

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
  • Primary Citation of Related Structures:  
    3E9U

  • 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 exchange activity ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Na/Ca exchange proteinA162Drosophila melanogasterMutation(s): 0 
Gene Names: CalxNCXCG5685
UniProt
Find proteins for Q24413 (Drosophila melanogaster)
Explore Q24413 
Go to UniProtKB:  Q24413
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.257 
  • R-Value Observed: 0.258 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.365α = 90
b = 113.365β = 90
c = 41.616γ = 120
Software Package:
Software NamePurpose
CrystalCleardata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

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

Revision History  (Full details and data files)

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