6MC9

Crystal Structure of Human Nav1.4 C-Terminal (1599-1754) domain in complex with calcium-bound calmodulin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.240 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Ca2+-dependent regulation of sodium channels NaV1.4 and NaV1.5 is controlled by the post-IQ motif.

Yoder, J.B.Ben-Johny, M.Farinelli, F.Srinivasan, L.Shoemaker, S.R.Tomaselli, G.F.Gabelli, S.B.Amzel, L.M.

(2019) Nat Commun 10: 1514-1514

  • DOI: 10.1038/s41467-019-09570-7
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Skeletal muscle voltage-gated Na <sup>+ </sup> channel (Na <sub>V </sub>1.4) activity is subject to calmodulin (CaM) mediated Ca <sup>2+ </sup>-dependent inactivation; no such inactivation is observed in the cardiac Na <sup>+ </sup> channel (Na <sub> ...

    Skeletal muscle voltage-gated Na + channel (Na V 1.4) activity is subject to calmodulin (CaM) mediated Ca 2+ -dependent inactivation; no such inactivation is observed in the cardiac Na + channel (Na V 1.5). Taken together, the crystal structures of the Na V 1.4 C-terminal domain relevant complexes and thermodynamic binding data presented here provide a rationale for this isoform difference. A Ca 2+ -dependent CaM N-lobe binding site previously identified in Na V 1.5 is not present in Na V 1.4 allowing the N-lobe to signal other regions of the Na V 1.4 channel. Consistent with this mechanism, removing this binding site in Na V 1.5 unveils robust Ca 2+ -dependent inactivation in the previously insensitive isoform. These findings suggest that Ca 2+ -dependent inactivation is effected by CaM's N-lobe binding outside the Na V C-terminal while CaM's C-lobe remains bound to the Na V C-terminal. As the N-lobe binding motif of Na V 1.5 is a mutational hotspot for inherited arrhythmias, the contributions of mutation-induced changes in CDI to arrhythmia generation is an intriguing possibility.


    Organizational Affiliation

    Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, 10032, USA.,Division of Cardiology, Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.,Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA. gabelli@jhmi.edu.,Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA. gabelli@jhmi.edu.,Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.,Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA. gabelli@jhmi.edu.,Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.,Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA. mamzel@jhmi.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Sodium channel protein type 4 subunit alpha
A
168Homo sapiensMutation(s): 0 
Gene Names: SCN4A
Find proteins for P35499 (Homo sapiens)
Go to Gene View: SCN4A
Go to UniProtKB:  P35499
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Calmodulin-1
B
149Rattus norvegicusMutation(s): 0 
Gene Names: Calm1 (Calm, Cam, Cam1, CaMI)
Find proteins for P0DP29 (Rattus norvegicus)
Go to UniProtKB:  P0DP29
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.240 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 72.615α = 90.00
b = 72.615β = 90.00
c = 134.661γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Heart, Lung, and Blood InstituteUnited States5R01HL128743

Revision History 

  • Version 1.0: 2019-04-10
    Type: Initial release
  • Version 1.1: 2019-04-17
    Type: Data collection, Database references