3RB7 | pdb_00003rb7

Crystal structure of CBD12 from CALX1.2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 
    0.278 (Depositor), 0.266 (DCC) 
  • R-Value Work: 
    0.231 (Depositor), 0.228 (DCC) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3RB7

This is version 1.1 of the entry. See complete history

Literature

Structural Basis of the Ca(2+) Inhibitory Mechanism of Drosophila Na(+)/Ca(2+) Exchanger CALX and Its Modification by Alternative Splicing.

Wu, M.Tong, S.Gonzalez, J.Jayaraman, V.Spudich, J.L.Zheng, L.

(2011) Structure 19: 1509-1517

  • DOI: https://doi.org/10.1016/j.str.2011.07.008
  • Primary Citation Related Structures: 
    3RB5, 3RB7

  • PubMed Abstract: 

    The Na(+)/Ca(2+) exchanger CALX promotes Ca(2+) efflux in Drosophila sensory neuronal cells to facilitate light-mediated Ca(2+) homeostasis. CALX activity is negatively regulated by specific Ca(2+) interaction within its two intracellular Ca(2+) regulatory domains CBD1 and CBD2, yet how the Ca(2+) binding is converted to molecular motion to operate the exchanger is unknown. Here, we report crystal structures of the entire Ca(2+) regulatory domain CBD12 from two alternative splicing isoforms, CALX 1.1 and 1.2, exhibiting distinct regulatory Ca(2+) dependency. The structures show an open V-shaped conformation with four Ca(2+) ions bound on the CBD domain interface, confirmed by LRET analysis. The structures together with Ca(2+)-binding analysis support that the Ca(2+) inhibition of CALX is achieved by interdomain conformational changes induced by Ca(2+) binding at CBD1. The conformational difference between the two isoforms also indicates that alternative splicing adjusts the interdomain orientation angle to modify the Ca(2+) regulatory property of the exchangers.


  • Organizational Affiliation
    • Center for Membrane Biology, Department of Biochemistry and Molecular Biology, The University of Texas Houston Medical School, Houston, TX 77030, USA.

Macromolecule Content 

  • Total Structure Weight: 136.2 kDa 
  • Atom Count: 7,969 
  • Modeled Residue Count: 982 
  • Deposited Residue Count: 1,192 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Na/Ca exchange proteinA,
B,
C [auth E],
D [auth G]
298Drosophila melanogasterMutation(s): 0 
Gene Names: CalxNCXCG5685
UniProt
Find proteins for Q9VDG5 (Drosophila melanogaster)
Explore Q9VDG5 
Go to UniProtKB:  Q9VDG5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9VDG5
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
I [auth A],
J [auth B],
S [auth E],
X [auth G]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CA

Query on CA



Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
G [auth A]
H [auth A]
K [auth B]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
O [auth E],
P [auth E],
Q [auth E],
R [auth E],
T [auth G],
U [auth G],
V [auth G],
W [auth G]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free:  0.278 (Depositor), 0.266 (DCC) 
  • R-Value Work:  0.231 (Depositor), 0.228 (DCC) 
Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.535α = 90
b = 107.535β = 90
c = 358.65γ = 120
Software Package:
Software NamePurpose
CrystalCleardata collection
PHASERphasing
PHENIXrefinement
d*TREKdata reduction
d*TREKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-11-02
    Type: Initial release
  • Version 1.1: 2024-02-21
    Changes: Data collection, Database references, Derived calculations