Structure of Sodium/Calcium Exchanger from Methanococcus jannaschii

Experimental Data Snapshot

  • Resolution: 3.50 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.281 
  • R-Value Observed: 0.282 

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Structural insight into the ion-exchange mechanism of the sodium/calcium exchanger.

Liao, J.Li, H.Zeng, W.Sauer, D.B.Belmares, R.Jiang, Y.

(2012) Science 335: 686-690

  • DOI: https://doi.org/10.1126/science.1215759
  • Primary Citation of Related Structures:  
    3V5S, 3V5U

  • PubMed Abstract: 

    Sodium/calcium (Na(+)/Ca(2+)) exchangers (NCX) are membrane transporters that play an essential role in maintaining the homeostasis of cytosolic Ca(2+) for cell signaling. We demonstrated the Na(+)/Ca(2+)-exchange function of an NCX from Methanococcus jannaschii (NCX_Mj) and report its 1.9 angstrom crystal structure in an outward-facing conformation. Containing 10 transmembrane helices, the two halves of NCX_Mj share a similar structure with opposite orientation. Four ion-binding sites cluster at the center of the protein: one specific for Ca(2+) and three that likely bind Na(+). Two passageways allow for Na(+) and Ca(2+) access to the central ion-binding sites from the extracellular side. Based on the symmetry of NCX_Mj and its ability to catalyze bidirectional ion-exchange reactions, we propose a structure model for the inward-facing NCX_Mj.

  • Organizational Affiliation

    Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9040, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sodium/Calcium Exchanger320Methanocaldococcus jannaschii DSM 2661Mutation(s): 1 
Gene Names: MJ0091
Membrane Entity: Yes 
Find proteins for Q57556 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Explore Q57556 
Go to UniProtKB:  Q57556
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ57556
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.50 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.281 
  • R-Value Observed: 0.282 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.99α = 90
b = 84.99β = 90
c = 181.634γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-02-22
    Type: Initial release
  • Version 1.1: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description