Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction | Predict Membrane 

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

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

Macromolecule Content

• Total Structure Weight: 38.56 kDa 
• Atom Count: 2590 
• Modelled Residue Count: 297 
• Deposited Residue Count: 320 
• Unique protein chains: 1

3V5U

Structure of Sodium/Calcium Exchanger from Methanocaldococcus jannaschii DSM 2661

• PDB DOI: 10.2210/pdb3V5U/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): Jiang, Y., Liao, J., Li, H., Zeng, W., Sauer, D., Belmares, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.210 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 

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: 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized membrane protein MJ0091	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 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OLC	K [auth A], L [auth A], M [auth A], X [auth A], Y [auth A]	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C21 H40 O4 RZRNAYUHWVFMIP-GDCKJWNLSA-N
1PE	Q [auth A]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
MYS	N [auth A], O [auth A], P [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A]	PENTADECANE C15 H32 YCOZIPAWZNQLMR-UHFFFAOYSA-N
ACT	G [auth A], H [auth A], I [auth A], J [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA	C [auth A], F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA	B [auth A], D [auth A], E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.210 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.49	α = 90
b = 72.879	β = 90
c = 96.206	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
SHARP	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2012-02-22
  Type: Initial release