6MUE

Voltage-gated sodium channel NaV1.4 IQ domain in complex with Ca2+/Calmodulin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structures of Ca2+-calmodulin bound to NaVC-terminal regions suggest role for EF-hand domain in binding and inactivation.

Gardill, B.R.Rivera-Acevedo, R.E.Tung, C.C.Van Petegem, F.

(2019) Proc.Natl.Acad.Sci.USA 116: 10763-10772

  • DOI: 10.1073/pnas.1818618116
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Voltage-gated sodium (Na <sub>V </sub>) and calcium channels (Ca <sub>V </sub>) form targets for calmodulin (CaM), which affects channel inactivation properties. A major interaction site for CaM resides in the C-terminal (CT) region, consisting of an ...

    Voltage-gated sodium (Na V ) and calcium channels (Ca V ) form targets for calmodulin (CaM), which affects channel inactivation properties. A major interaction site for CaM resides in the C-terminal (CT) region, consisting of an IQ domain downstream of an EF-hand domain. We present a crystal structure of fully Ca 2+ -occupied CaM, bound to the CT of Na V 1.5. The structure shows that the C-terminal lobe binds to a site ∼90° rotated relative to a previous site reported for an apoCaM complex with the Na V 1.5 CT and for ternary complexes containing fibroblast growth factor homologous factors (FHF). We show that the binding of FHFs forces the EF-hand domain in a conformation that does not allow binding of the Ca 2+ -occupied C-lobe of CaM. These observations highlight the central role of the EF-hand domain in modulating the binding mode of CaM. The binding sites for Ca 2+ -free and Ca 2+ -occupied CaM contain targets for mutations linked to long-QT syndrome, a type of inherited arrhythmia. The related Na V 1.4 channel has been shown to undergo Ca 2+ -dependent inactivation (CDI) akin to Ca V s. We present a crystal structure of Ca 2+ /CaM bound to the Na V 1.4 IQ domain, which shows a binding mode that would clash with the EF-hand domain. We postulate the relative reorientation of the EF-hand domain and the IQ domain as a possible conformational switch that underlies CDI.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Life Sciences Institute, The University of British Columbia, Vancouver, BC, Canada V6T 1Z3.,Department of Biochemistry and Molecular Biology, Life Sciences Institute, The University of British Columbia, Vancouver, BC, Canada V6T 1Z3 filip.vanpetegem@gmail.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Calmodulin-1
A
151Homo sapiensMutation(s): 0 
Gene Names: CALM1 (CALM, CAM, CAM1)
Find proteins for P0DP23 (Homo sapiens)
Go to Gene View: CALM1
Go to UniProtKB:  P0DP23
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Sodium channel protein type 4 subunit alpha
B
29Rattus norvegicusMutation(s): 0 
Gene Names: Scn4a
Find proteins for P15390 (Rattus norvegicus)
Go to UniProtKB:  P15390
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.214 
  • Space Group: P 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 58.580α = 90.00
b = 24.433β = 112.63
c = 60.720γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata scaling
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health ResearchCanadaMOP-119404

Revision History 

  • Version 1.0: 2019-05-08
    Type: Initial release
  • Version 1.1: 2019-05-22
    Type: Data collection, Database references
  • Version 1.2: 2019-06-12
    Type: Data collection, Database references