4JQ0

Voltage-gated sodium channel 1.5 C-terminal domain in complex with FGF12B and Ca2+/calmodulin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.84 Å
  • R-Value Free: 0.320 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.257 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural analyses of Ca(2+)/CaM interaction with NaV channel C-termini reveal mechanisms of calcium-dependent regulation.

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

(2014) Nat Commun 5: 4896-4896

  • DOI: https://doi.org/10.1038/ncomms5896
  • Primary Citation of Related Structures:  
    4JPZ, 4JQ0

  • PubMed Abstract: 

    Ca(2+) regulates voltage-gated Na(+) (NaV) channels, and perturbed Ca(2+) regulation of NaV function is associated with epilepsy syndromes, autism and cardiac arrhythmias. Understanding the disease mechanisms, however, has been hindered by a lack of structural information and competing models for how Ca(2+) affects NaV channel function. Here we report the crystal structures of two ternary complexes of a human NaV cytosolic C-terminal domain (CTD), a fibroblast growth factor homologous factor and Ca(2+)/calmodulin (Ca(2+)/CaM). These structures rule out direct binding of Ca(2+) to the NaV CTD and uncover new contacts between CaM and the NaV CTD. Probing these new contacts with biochemical and functional experiments allows us to propose a mechanism by which Ca(2+) could regulate NaV channels. Further, our model provides hints towards understanding the molecular basis of the neurologic disorders and cardiac arrhythmias caused by NaV channel mutations.


  • Organizational Affiliation

    1] Ion Channel Research Unit, Department of Medicine, Duke University Medical Center, 2 Genome Court, Durham, North Carolina 27710, USA [2] Division of Cardiology, Department of Medicine, Duke University Medical Center, 2 Genome Court, Durham, North Carolina 27710, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fibroblast growth factor 12243Homo sapiensMutation(s): 0 
Gene Names: FGF12FGF12BFHF1
UniProt & NIH Common Fund Data Resources
Find proteins for P61328 (Homo sapiens)
Explore P61328 
Go to UniProtKB:  P61328
PHAROS:  P61328
GTEx:  ENSG00000114279 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61328
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CalmodulinB [auth C]149Homo 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
Sodium channel protein type 5 subunit alphaC [auth D]191Homo 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.84 Å
  • R-Value Free: 0.320 
  • R-Value Work: 0.253 
  • R-Value Observed: 0.257 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.2α = 90
b = 115.2β = 90
c = 120.11γ = 120
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: 2014-05-21
    Type: Initial release
  • Version 1.1: 2014-10-22
    Changes: Database references
  • Version 1.2: 2014-12-03
    Changes: Structure summary
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references, Derived calculations