4DCK

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


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 

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This is version 1.2 of the entry. See complete history


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

  • DOI: https://doi.org/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.


  • Organizational Affiliation

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sodium channel protein type 5 subunit alpha168Homo sapiensMutation(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 Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14524
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Calmodulin149Homo sapiensMutation(s): 0 
Gene Names: 
CALM1CALMCAMCAM1CALM2CAM2CAMBCALM3CALML2CAM3...
CALM1CALMCAMCAM1CALM2CAM2CAMBCALM3CALML2CAM3CAMCCAMIII

UniProt & NIH Common Fund Data Resources
Find proteins for P0DP23 (Homo sapiens)
Explore P0DP23 
Go to UniProtKB:  P0DP23
PHAROS:  P0DP23
GTEx:  ENSG00000198668 
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UniProt GroupP0DP23
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Fibroblast growth factor 13192Homo sapiensMutation(s): 0 
Gene Names: FGF13FHF2
UniProt & NIH Common Fund Data Resources
Find proteins for Q92913 (Homo sapiens)
Explore Q92913 
Go to UniProtKB:  Q92913
PHAROS:  Q92913
GTEx:  ENSG00000129682 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92913
Sequence Annotations
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  • Reference Sequence
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 = 126.041α = 90
b = 126.041β = 90
c = 126.041γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-06-27
    Type: Initial release
  • Version 1.1: 2012-07-25
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations