Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

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

Macromolecule Content

• Total Structure Weight: 21947.88 
• Atom Count: 1386 
• Residue Count: 187 
• Unique protein chains: 2

4DJC

1.35 A crystal structure of the NaV1.5 DIII-IV-Ca/CaM complex

• DOI: 10.2210/pdb4DJC/pdb

• Classification: calcium-binding protein
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2012-02-01 Released: 2012-02-22 
• Deposition Author(s): Sarhan, M.F., Tung, C.-C., Van Petegem, F., Ahern, C.A.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 0.176 
• R-Value Work: 0.153 

Literature

Crystallographic basis for calcium regulation of sodium channels.

Sarhan, M.F., Tung, C.C., Van Petegem, F., Ahern, C.A.

(2012) Proc.Natl.Acad.Sci.USA 109: 3558-3563

• PubMed: 22331908 
• DOI: 10.1073/pnas.1114748109


• PubMed Abstract: 
  

Voltage-gated sodium channels underlie the rapid regenerative upstroke of action potentials and are modulated by cytoplasmic calcium ions through a poorly understood mechanism. We describe the 1.35 Å crystal structure of Ca(2+)-bound calmodulin (Ca(2+)/CaM) in complex with the inactivation gate (DIII-IV linker) of the cardiac sodium channel (Na(V)1.5). The complex harbors the positions of five disease mutations involved with long Q-T type 3 and Brugada syndromes. In conjunction with isothermal titration calorimetry, we identify unique inactivation-gate mutations that enhance or diminish Ca(2+)/CaM binding, which, in turn, sensitize or abolish Ca(2+) regulation of full-length channels in electrophysiological experiments. Additional biochemical experiments support a model whereby a single Ca(2+)/CaM bridges the C-terminal IQ motif to the DIII-IV linker via individual N and C lobes, respectively. The data suggest that Ca(2+)/CaM destabilizes binding of the inactivation gate to its receptor, thus biasing inactivation toward more depolarized potentials.

---

Organizational Affiliation: 

Department of Anesthesiology, Pharmacology and Therapeutics, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada, V6T 1Z3.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Calmodulin	A	152	Homo sapiens	Mutation(s): 0  Gene Names: CALM3 (CALML2, CAM3, CAMC, CAMIII)
Find proteins for P0DP25 (Homo sapiens) Go to Gene View: CALM3 Go to UniProtKB:  P0DP25

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Sodium channel protein type 5 subunit alpha	B	35	Homo sapiens	Mutation(s): 0  Gene Names: SCN5A
Find proteins for Q14524 (Homo sapiens) Go to Gene View: SCN5A Go to UniProtKB:  Q14524

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
IPA	A	ISOPROPYL ALCOHOL 2-PROPANOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 0.176 
• R-Value Work: 0.153 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 28.380	α = 90.00
b = 72.720	β = 90.00
c = 97.010	γ = 90.00

Software Package:

Software Name	Purpose
XSCALE	data scaling
XDS	data reduction
PHASER	phasing
XDS	data scaling
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-02-01 
• Released Date: 2012-02-22 
• Deposition Author(s): Sarhan, M.F., Tung, C.-C., Van Petegem, F., Ahern, C.A.

Revision History 

• Version 1.0: 2012-02-22
  Type: Initial release
• Version 1.1: 2012-03-21
  Type: Database references
• Version 1.2: 2018-01-24
  Type: Structure summary