3V5U

Structure of Sodium/Calcium Exchanger from Methanocaldococcus jannaschii DSM 2661


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 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


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

  • 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Uncharacterized membrane protein MJ0091320Methanocaldococcus jannaschii DSM 2661Mutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ57556
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OLC
Query on OLC

Download Ideal Coordinates CCD File 
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
Query on 1PE

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Q [auth A]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
MYS
Query on MYS

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N [auth A]
O [auth A]
P [auth A]
R [auth A]
S [auth A]
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
Query on ACT

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G [auth A],
H [auth A],
I [auth A],
J [auth A]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA
Query on CA

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C [auth A],
F [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA
Query on NA

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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 = 49.49α = 90
b = 72.879β = 90
c = 96.206γ = 90
Software Package:
Software NamePurpose
HKL-3000data collection
SHARPphasing
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-02-22
    Type: Initial release
  • Version 1.1: 2024-02-28
    Changes: Data collection, Database references, Derived calculations