3V5S | pdb_00003v5s

Structure of Sodium/Calcium Exchanger from Methanococcus jannaschii

• PDB DOI: https://doi.org/10.2210/pdb3V5S/pdb

• Classification: METAL TRANSPORT
• Organism(s): Methanocaldococcus jannaschii DSM 2661
• Expression System: Escherichia coli
• Mutation(s): Yes 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2011-12-16 Released: 2012-02-22 
• Deposition Author(s): Liao, J., Li, H., Zeng, W., Sauer, D.B., Belmares, R., Jiang, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 
  0.303 (Depositor), 0.315 (DCC) 
• R-Value Work: 
  0.281 (Depositor), 0.286 (DCC) 
• R-Value Observed: 
  0.282 (Depositor) 

Starting Model: experimental

Literature

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

• PubMed: 22323814 
• DOI: https://doi.org/10.1126/science.1215759
• Primary Citation 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.

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 34.47 kDa 
• Atom Count: 2,172 
• Modeled Residue Count: 289 
• Deposited Residue Count: 320 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sodium/Calcium Exchanger	A	320	Methanocaldococcus jannaschii DSM 2661	Mutation(s): 1  Gene Names: MJ0091 Membrane Entity: Yes
UniProt
Find proteins for Q57556 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q57556  Go to UniProtKB:  Q57556

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CD	B [auth A], C [auth A]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free:  0.303 (Depositor), 0.315 (DCC) 
• R-Value Work:  0.281 (Depositor), 0.286 (DCC) 
• R-Value Observed: 0.282 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.99	α = 90
b = 84.99	β = 90
c = 181.634	γ = 90

Software Package:

Software Name	Purpose
PHASES	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-02-22 
Deposition Author(s): Liao, J., Li, H., Zeng, W., Sauer, D.B., Belmares, R., Jiang, Y.

Revision History  

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