6MC9 | pdb_00006mc9

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

• PDB DOI: https://doi.org/10.2210/pdb6MC9/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens, Rattus norvegicus
• Expression System: Escherichia coli BL21
• Mutation(s): No 
• Membrane Protein: Yes  mpstruc


• Deposited: 2018-08-30 Released: 2019-04-10 
• Deposition Author(s): Yoder, J.B., Gabelli, S.B., Amzel, L.M.
• Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 
  0.285 (Depositor), 0.285 (DCC) 
• R-Value Work: 
  0.240 (Depositor), 0.242 (DCC) 
• R-Value Observed: 
  0.242 (Depositor) 

Starting Model: experimental

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

• PubMed: 30944319 
• DOI: https://doi.org/10.1038/s41467-019-09570-7
• Primary Citation Related Structures: 
  6MBA, 6MC9


• PubMed Abstract: 
  

  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.

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Organizational Affiliation: 
• Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, 10032, USA.
Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
Division of Cardiology, Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, 10461, USA.
Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA. [e-mail].
Division of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA. [e-mail].
Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA. [e-mail].
Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: isothermal titration calorimetry

Macromolecule Content 

• Total Structure Weight: 36.22 kDa 
• Atom Count: 2,330 
• Modeled Residue Count: 291 
• Deposited Residue Count: 317 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sodium channel protein type 4 subunit alpha	A	168	Homo sapiens	Mutation(s): 0  Gene Names: SCN4A Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P35499 (Homo sapiens) Explore P35499  Go to UniProtKB:  P35499
PHAROS:  P35499 GTEx:  ENSG00000007314

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Calmodulin-1	B	149	Rattus norvegicus	Mutation(s): 0  Gene Names: Calm1, Calm, Cam, Cam1, CaMI
UniProt
Find proteins for P0DP29 (Rattus norvegicus) Explore P0DP29  Go to UniProtKB:  P0DP29

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	C [auth B], D [auth B], E [auth B], F [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free:  0.285 (Depositor), 0.285 (DCC) 
• R-Value Work:  0.240 (Depositor), 0.242 (DCC) 
• R-Value Observed: 0.242 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.615	α = 90
b = 72.615	β = 90
c = 134.661	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-04-10 
Deposition Author(s): Yoder, J.B., Gabelli, S.B., Amzel, L.M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	5R01HL128743

Revision History  

• Version 1.0: 2019-04-10
  Type: Initial release
  
• Version 1.1: 2019-04-17
  Changes: Data collection, Database references
• Version 1.2: 2019-12-04
  Changes: Author supporting evidence
• Version 1.3: 2023-10-11
  Changes: Data collection, Database references, Refinement description