5JDL

Structural mechanisms of extracellular ion exchange and induced binding-site occlusion in the sodium-calcium exchanger NCX_Mj soaked with 2.5 mM Na+ and 1mM Sr2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.229 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Mechanism of extracellular ion exchange and binding-site occlusion in a sodium/calcium exchanger.

Liao, J.Marinelli, F.Lee, C.Huang, Y.Faraldo-Gomez, J.D.Jiang, Y.

(2016) Nat Struct Mol Biol 23: 590-599

  • DOI: 10.1038/nsmb.3230
  • Primary Citation of Related Structures:  
    5JDH, 5JDG, 5JDL, 5JDN, 5JDM, 5JDF, 5JDQ, 5HXC, 5HWY, 5HWX, 5HYA, 5HXR, 5HXS, 5HXE, 5HXH

  • PubMed Abstract: 
  • Na(+)/Ca(2+) exchangers use the Na(+) electrochemical gradient across the plasma membrane to extrude intracellular Ca(2+) and play a central role in Ca(2+) homeostasis. Here, we elucidate their mechanisms of extracellular ion recognition and exchange through a structural analysis of the exchanger from Methanococcus jannaschii (NCX_Mj) bound to Na(+), Ca(2+) or Sr(2+) in various occupancies and in an apo state ...

    Na(+)/Ca(2+) exchangers use the Na(+) electrochemical gradient across the plasma membrane to extrude intracellular Ca(2+) and play a central role in Ca(2+) homeostasis. Here, we elucidate their mechanisms of extracellular ion recognition and exchange through a structural analysis of the exchanger from Methanococcus jannaschii (NCX_Mj) bound to Na(+), Ca(2+) or Sr(2+) in various occupancies and in an apo state. This analysis defines the binding mode and relative affinity of these ions, establishes the structural basis for the anticipated 3:1 Na(+)/Ca(2+)-exchange stoichiometry and reveals the conformational changes at the onset of the alternating-access transport mechanism. An independent analysis of the dynamics and conformational free-energy landscape of NCX_Mj in different ion-occupancy states, based on enhanced-sampling molecular dynamics simulations, demonstrates that the crystal structures reflect mechanistically relevant, interconverting conformations. These calculations also reveal the mechanism by which the outward-to-inward transition is controlled by the ion occupancy, thereby explaining the emergence of strictly coupled Na(+)/Ca(2+) antiport.


    Related Citations: 
    • 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

    Organizational Affiliation

    Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Uncharacterized membrane protein MJ0091A301Methanocaldococcus 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OLC (Subject of Investigation/LOI)
Query on OLC

Download Ideal Coordinates CCD File 
E [auth A], F [auth A], G [auth A], H [auth A](2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
 Ligand Interaction
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
L [auth A]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
MYS (Subject of Investigation/LOI)
Query on MYS

Download Ideal Coordinates CCD File 
I [auth A], J [auth A], K [auth A]PENTADECANE
C15 H32
YCOZIPAWZNQLMR-UHFFFAOYSA-N
 Ligand Interaction
SR
Query on SR

Download Ideal Coordinates CCD File 
B [auth A], C [auth A]STRONTIUM ION
Sr
PWYYWQHXAPXYMF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
D [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.229 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.764α = 90
b = 72.622β = 90
c = 95.616γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United Statesfunding for Youxing Jiang
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM079179
Welch FoundationUnited StatesGrant I-1578
National Natural Science Foundation of China (NSFC)ChinaProject 31470817
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United Statesfunding for Jose D. Faraldo-Gomez

Revision History  (Full details and data files)

  • Version 1.0: 2016-05-11
    Type: Initial release
  • Version 1.1: 2016-06-01
    Changes: Database references
  • Version 1.2: 2016-06-15
    Changes: Database references
  • Version 1.3: 2017-09-20
    Changes: Author supporting evidence, Derived calculations
  • Version 1.4: 2019-11-20
    Changes: Author supporting evidence