2KAV | pdb_00002kav

Solution structure of the human Voltage-gated Sodium Channel, brain isoform (Nav1.2)


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 15 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report

Validation slider image for 2KAV

This is version 1.3 of the entry. See complete history

Literature

Solution structure of the NaV1.2 C-terminal EF-hand domain.

Miloushev, V.Z.Levine, J.A.Arbing, M.A.Hunt, J.F.Pitt, G.S.Palmer, A.G.

(2009) J Biological Chem 284: 6446-6454

  • DOI: https://doi.org/10.1074/jbc.M807401200
  • Primary Citation Related Structures: 
    2KAV

  • PubMed Abstract: 

    Voltage-gated sodium channels initiate the rapid upstroke of action potentials in many excitable tissues. Mutations within intracellular C-terminal sequences of specific channels underlie a diverse set of channelopathies, including cardiac arrhythmias and epilepsy syndromes. The three-dimensional structure of the C-terminal residues 1777-1882 of the human NaV1.2 voltage-gated sodium channel has been determined in solution by NMR spectroscopy at pH 7.4 and 290.5 K. The ordered structure extends from residues Leu-1790 to Glu-1868 and is composed of four alpha-helices separated by two short anti-parallel beta-strands; a less well defined helical region extends from residue Ser-1869 to Arg-1882, and a disordered N-terminal region encompasses residues 1777-1789. Although the structure has the overall architecture of a paired EF-hand domain, the NaV1.2 C-terminal domain does not bind Ca2+ through the canonical EF-hand loops, as evidenced by monitoring 1H,15N chemical shifts during aCa2+ titration. Backbone chemical shift resonance assignments and Ca2+ titration also were performed for the NaV1.5 (1773-1878) isoform, demonstrating similar secondary structure architecture and the absence of Ca2+ binding by the EF-hand loops. Clinically significant mutations identified in the C-terminal region of NaV1 sodium channels cluster in the helix I-IV interface and the helix II-III interhelical segment or in helices III and IV of the NaV1.2 (1777-1882) structure.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032-3702, USA.

Macromolecule Content 

  • Total Structure Weight: 14.59 kDa 
  • Atom Count: 851 
  • Modeled Residue Count: 106 
  • Deposited Residue Count: 129 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Sodium channel protein type 2 subunit alpha129Homo sapiensMutation(s): 0 
Gene Names: NAC2SCN2ASCN2A1SCN2A2
UniProt & NIH Common Fund Data Resources
Find proteins for Q99250 (Homo sapiens)
Explore Q99250 
Go to UniProtKB:  Q99250
PHAROS:  Q99250
GTEx:  ENSG00000136531 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99250
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 15 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-01-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2022-03-16
    Changes: Data collection, Database references, Derived calculations
  • Version 1.3: 2024-05-22
    Changes: Data collection