5F6T

Structure of calexcitin-Gd3+ complex.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.219 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Binding of Gd(3+) to the neuronal signalling protein calexcitin identifies an exchangeable Ca(2+)-binding site.

Chataigner, L.Guo, J.Erskine, P.T.Coker, A.R.Wood, S.P.Gombos, Z.Cooper, J.B.

(2016) Acta Crystallogr F Struct Biol Commun 72: 276-281

  • DOI: https://doi.org/10.1107/S2053230X16003526
  • Primary Citation of Related Structures:  
    5F6T

  • PubMed Abstract: 

    Calexcitin was first identified in the marine snail Hermissenda crassicornis as a neuronal-specific protein that becomes upregulated and phosphorylated in associative learning. Calexcitin possesses four EF-hand motifs, but only the first three (EF-1 to EF-3) are involved in binding metal ions. Past work has indicated that under physiological conditions EF-1 and EF-2 bind Mg(2+) and Ca(2+), while EF-3 is likely to bind only Ca(2+). The fourth EF-hand is nonfunctional owing to a lack of key metal-binding residues. The aim of this study was to use a crystallographic approach to determine which of the three metal-binding sites of calexcitin is most readily replaced by exogenous metal ions, potentially shedding light on which of the EF-hands play a `sensory' role in neuronal calcium signalling. By co-crystallizing recombinant calexcitin with equimolar Gd(3+) in the presence of trace Ca(2+), EF-1 was shown to become fully occupied by Gd(3+) ions, while the other two sites remain fully occupied by Ca(2+). The structure of the Gd(3+)-calexcitin complex has been refined to an R factor of 21.5% and an Rfree of 30.4% at 2.2 Å resolution. These findings suggest that EF-1 of calexcitin is the Ca(2+)-binding site with the lowest selectivity for Ca(2+), and the implications of this finding for calcium sensing in neuronal signalling pathways are discussed.


  • Organizational Affiliation

    Division of Medicine, UCL, Gower Street, London WC1E 6BT, England.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Calexcitin191Doryteuthis pealeiiMutation(s): 0 
Gene Names: cex
UniProt
Find proteins for O76764 (Doryteuthis pealeii)
Explore O76764 
Go to UniProtKB:  O76764
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO76764
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.304 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.219 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.02α = 90
b = 77.02β = 90
c = 29.26γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-12-16
    Type: Initial release
  • Version 1.1: 2016-02-10
    Changes: Database references, Structure summary
  • Version 1.2: 2016-04-13
    Changes: Database references
  • Version 1.3: 2016-07-20
    Changes: Database references
  • Version 1.4: 2024-01-10
    Changes: Data collection, Database references, Refinement description