2DPK | pdb_00002dpk

The Crystal Structure of the Primary Ca2+ Sensor of the Na+/Ca2+ Exchanger

• PDB DOI: https://doi.org/10.2210/pdb2DPK/pdb

• Classification: METAL TRANSPORT
• Organism(s): Canis lupus familiaris
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-05-12 Released: 2006-06-13 
• Deposition Author(s): Abramson, J., Sawaya, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.284 (Depositor) 
• R-Value Work: 
  0.222 (Depositor) 
• R-Value Observed: 
  0.225 (Depositor) 

Literature

The crystal structure of the primary Ca2+ sensor of the na+/ca2+ exchanger reveals a novel Ca2+ binding motif.

Nicoll, D.A., Sawaya, M., Kwon, S., Cascio, D., Philipson, K.D., Abramson, J.

(2006) J Biological Chem 281: 21577-21581

• PubMed: 16774926 
• DOI: https://doi.org/10.1074/jbc.C600117200
• Primary Citation Related Structures: 
  2DPK


• PubMed Abstract: 
  

  The Na+/Ca2+ exchanger is a plasma membrane protein that regulates intracellular Ca2+ levels in cardiac myocytes. Transport activity is governed by Ca2+, and the primary Ca2+ sensor (CBD1) is located in a large cytoplasmic loop connecting two transmembrane helices. The binding of Ca2+ to the CBD1 sensory domain results in conformational changes that stimulate the exchanger to extrude Ca2+. Here, we present a crystal structure of CBD1 at 2.5A resolution, which reveals a novel Ca2+ binding site consisting of four Ca2+ ions arranged in a tight planar cluster. This intricate coordination pattern for a Ca2+ binding cluster is indicative of a highly sensitive Ca2+ sensor and may represent a general platform for Ca2+ sensing.

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Organizational Affiliation: 
• Department of Physiology and the Cardiovascular Research Laboratories, David Geffen School of Medicine, University of California, Los Angeles, California 90095.
Department of Chemistry and Biochemistry, UCLA-Department of Energy Center for Genomics and Proteomics, Molecular Biology Institute, University of California, Los Angeles, California 90095.
Department of Physiology and the Cardiovascular Research Laboratories, David Geffen School of Medicine, University of California, Los Angeles, California 90095. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 17.15 kDa 
• Atom Count: 984 
• Modeled Residue Count: 124 
• Deposited Residue Count: 152 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sodium/calcium exchanger 1	A	152	Canis lupus familiaris	Mutation(s): 0
UniProt
Find proteins for P23685 (Canis lupus familiaris) Explore P23685  Go to UniProtKB:  P23685

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE	G [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
GAI	F [auth A]	GUANIDINE C H5 N3 ZRALSGWEFCBTJO-UHFFFAOYSA-N
CA	B [auth A], C [auth A], D [auth A], E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.284 (Depositor) 
• R-Value Work:  0.222 (Depositor) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.624	α = 90
b = 45.524	β = 90
c = 57.269	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-06-13 
Deposition Author(s): Abramson, J., Sawaya, M.

Revision History  

• Version 1.0: 2006-06-13
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-10-23
  Changes: Data collection, Database references, Derived calculations, Structure summary