Biological Assembly 1  

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

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 33.10 kDa 
• Atom Count: 1905 
• Modelled Residue Count: 249 
• Deposited Residue Count: 295 
• Unique protein chains: 1

3US9

Crystal Structure of the NCX1 Intracellular Tandem Calcium Binding Domains(CBD12)

• PDB DOI: 10.2210/pdb3US9/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Canis lupus familiaris
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2011-11-23 Released: 2012-07-11 
• Deposition Author(s): Giladi, M., Sasson, Y., Hirsch, J.A., Khananshvili, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.68 Å
• R-Value Free: 0.274 
• R-Value Work: 0.234 

Literature

A common Ca2+-driven interdomain module governs eukaryotic NCX regulation.

Giladi, M., Sasson, Y., Fang, X., Hiller, R., Buki, T., Wang, Y.X., Hirsch, J.A., Khananshvili, D.

(2012) PLoS One 7: e39985-e39985

• PubMed: 22768191 
• DOI: 10.1371/journal.pone.0039985
• Primary Citation of Related Structures:  
  3US9


• PubMed Abstract: 
  

Na(+)/Ca(2+) exchanger (NCX) proteins mediate Ca(2+)-fluxes across the cell membrane to maintain Ca(2+) homeostasis in many cell types. Eukaryotic NCX contains Ca(2+)-binding regulatory domains, CBD1 and CBD2. Ca(2+) binding to a primary sensor (Ca3-Ca4 sites) on CBD1 activates mammalian NCXs, whereas CALX, a Drosophila NCX ortholog, displays an inhibitory response to regulatory Ca(2+). To further elucidate the underlying regulatory mechanisms, we determined the 2.7 Å crystal structure of mammalian CBD12-E454K, a two-domain construct that retains wild-type properties. In conjunction with stopped-flow kinetics and SAXS (small-angle X-ray scattering) analyses of CBD12 mutants, we show that Ca(2+) binding to Ca3-Ca4 sites tethers the domains via a network of interdomain salt-bridges. This Ca(2+)-driven interdomain switch controls slow dissociation of "occluded" Ca(2+) from the primary sensor and thus dictates Ca(2+) sensing dynamics. In the Ca(2+)-bound conformation, the interdomain angle of CBD12 is very similar in NCX and CALX, meaning that the interdomain distances cannot account for regulatory diversity in NCX and CALX. Since the two-domain interface is nearly identical among eukaryotic NCXs, including CALX, we suggest that the Ca(2+)-driven interdomain switch described here represents a general mechanism for initial conduction of regulatory signals in NCX variants.

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Organizational Affiliation: 

Department of Physiology and Pharmacology, Sackler School of Medicine, Tel-Aviv University, Ramat-Aviv, Tel-Aviv, Israel.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sodium/calcium exchanger 1	A	295	Canis lupus familiaris	Mutation(s): 1  Gene Names: SLC8A1
UniProt
Find proteins for P23685 (Canis lupus familiaris) Explore P23685  Go to UniProtKB:  P23685

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	B [auth A], C [auth A], D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.68 Å
• R-Value Free: 0.274 
• R-Value Work: 0.234 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.67	α = 90
b = 152.55	β = 90
c = 79.7	γ = 90

Software Package:

Software Name	Purpose
DNA	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-11-23 
• Released Date: 2012-07-11 
Deposition Author(s): Giladi, M., Sasson, Y., Hirsch, J.A., Khananshvili, D.

Revision History  

• Version 1.0: 2012-07-11
  Type: Initial release
  
• Version 1.1: 2017-08-16
  Changes: Data collection, Refinement description, Source and taxonomy
• Version 1.2: 2020-01-01
  Changes: Database references