5DBR | pdb_00005dbr

Ca2+ CaM with human cardiac Na+ channel (NaV1.5) inactivation gate

• PDB DOI: https://doi.org/10.2210/pdb5DBR/pdb

• Classification: Metal Binding Protein/Transport Protein
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3), Escherichia coli
• Mutation(s): No 


• Deposited: 2015-08-21 Released: 2017-02-22 
• Deposition Author(s): Johnson, C.N., Thompson, M.K., Chazin, W.J.
• Funding Organization(s): Vanderbilt University, National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS), National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI), American Heart Association

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 
  0.284 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.224 (Depositor) 

Starting Model: experimental

Literature

Enhanced Understanding of Ca2+ Modulation of the Human Cardiac Sodium Channel: Tight Binding of Calmodulin to the Inactivation Gate

Johnson, C.N., Thompson, M.K., Voehler, M., Chazin, W.J.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 22.47 kDa 
• Atom Count: 1,212 
• Modeled Residue Count: 159 
• Deposited Residue Count: 196 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Calmodulin	A	145	Homo sapiens	Mutation(s): 0  Gene Names:  CALM1, CALM, CAM, CAM1, CALM2, CAM2, CAMB, CALM3, CALML2, CAM3, CAMC, CAMIII
UniProt & NIH Common Fund Data Resources
Find proteins for P0DP23 (Homo sapiens) Explore P0DP23  Go to UniProtKB:  P0DP23
PHAROS:  P0DP23 GTEx:  ENSG00000198668

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Sodium channel protein type 5 subunit alpha	B [auth C]	51	Homo sapiens	Mutation(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

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free:  0.284 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.224 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.086	α = 90
b = 58.086	β = 90
c = 102.638	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
PROTEUM PLUS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-02-22 
Deposition Author(s): Johnson, C.N., Thompson, M.K., Chazin, W.J.

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Funding Organization	Location	Grant Number
Vanderbilt University	United States	Endowed Chair to WJC
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	NRSA 2T32NS007491-11
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	NRSA 5 F32 HL117612-02
American Heart Association	United States	13POST14380036

Revision History  

• Version 1.0: 2017-02-22
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Author supporting evidence
• Version 1.2: 2017-10-04
  Changes: Author supporting evidence
• Version 1.3: 2019-12-04
  Changes: Author supporting evidence
• Version 1.4: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description