Biological Assembly 1  

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

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Biological Assembly 2  

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

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Hetero 9-mer - A3B3C3 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 57.90 kDa 
• Atom Count: 3693 
• Modelled Residue Count: 435 
• Deposited Residue Count: 509 
• Unique protein chains: 3

4DCK

Crystal structure of the C-terminus of voltage-gated sodium channel in complex with FGF13 and CaM

• PDB DOI: 10.2210/pdb4DCK/pdb

• Classification: TRANSPORT PROTEIN/SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-01-17 Released: 2012-06-27 
• Deposition Author(s): Chung, B.C., Wang, C., Yan, H., Pitt, G.S., Lee, S.Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.227 
• R-Value Work: 0.210 
• R-Value Observed: 0.211 

Literature

Crystal Structure of the Ternary Complex of a NaV C-Terminal Domain, a Fibroblast Growth Factor Homologous Factor, and Calmodulin.

Wang, C., Chung, B.C., Yan, H., Lee, S.Y., Pitt, G.S.

(2012) Structure 20: 1167-1176

• PubMed: 22705208 
• DOI: 10.1016/j.str.2012.05.001
• Primary Citation of Related Structures:  
  4DCK


• PubMed Abstract: 
  

Voltage-gated Na⁺ (Na(V)) channels initiate neuronal action potentials. Na(V) channels are composed of a transmembrane domain responsible for voltage-dependent Na⁺ conduction and a cytosolic C-terminal domain (CTD) that regulates channel function through interactions with many auxiliary proteins, including fibroblast growth factor homologous factors (FHFs) and calmodulin (CaM). Most ion channel structural studies have focused on mechanisms of permeation and voltage-dependent gating but less is known about how intracellular domains modulate channel function. Here we report the crystal structure of the ternary complex of a human Na(V) CTD, an FHF, and Ca²⁺-free CaM at 2.2 Å. Combined with functional experiments based on structural insights, we present a platform for understanding the roles of these auxiliary proteins in Na(V) channel regulation and the molecular basis of mutations that lead to neuronal and cardiac diseases. Furthermore, we identify a critical interaction that contributes to the specificity of individual Na(V) CTD isoforms for distinctive FHFs.

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Organizational Affiliation: 

Division of Cardiology, Department of Medicine, Duke University Medical Center, 2 Genome Ct, Durham, NC 27710, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sodium channel protein type 5 subunit alpha	A	168	Homo sapiens	Mutation(s): 0  Gene Names: SCN5A
UniProt & NIH Common Fund Data Resources
Find proteins for Q14524 (Homo sapiens) Explore Q14524  Go to UniProtKB:  Q14524
PHAROS:  Q14524 GTEx:  ENSG00000183873

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Calmodulin	B	149	Homo sapiens	Mutation(s): 0  Gene Names:  CALM1, CALM, CAM, CAM1, CALM2, CAM2, CAMB, CALM3, CALML2, CAM3, CAMC, CAMIII
UniProt & NIH Common Fund Data Resources
Find proteins for P0DP23 (Homo sapiens) Explore P0DP23  Go to UniProtKB:  P0DP23
PHAROS:  P0DP23 GTEx:  ENSG00000198668

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fibroblast growth factor 13	C	192	Homo sapiens	Mutation(s): 0  Gene Names: FGF13, FHF2
UniProt & NIH Common Fund Data Resources
Find proteins for Q92913 (Homo sapiens) Explore Q92913  Go to UniProtKB:  Q92913
PHAROS:  Q92913 GTEx:  ENSG00000129682

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	D [auth B], E [auth B], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.227 
• R-Value Work: 0.210 
• R-Value Observed: 0.211 
• Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.041	α = 90
b = 126.041	β = 90
c = 126.041	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-01-17 
• Released Date: 2012-06-27 
Deposition Author(s): Chung, B.C., Wang, C., Yan, H., Pitt, G.S., Lee, S.Y.

Revision History  

• Version 1.0: 2012-06-27
  Type: Initial release
  
• Version 1.1: 2012-07-25
  Changes: Database references