6BYO

Residue assignment correction to the voltage gated calcium Cav1.1 rabbit alpha 1 subunit PDB entries 3JBR & 5GJV

• PDB DOI: https://doi.org/10.2210/pdb6BYO/pdb
• EM Map EMD-9513: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Oryctolagus cuniculus
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMD


• Deposited: 2017-12-21 Released: 2018-05-02 
• Deposition Author(s): Cardozo, T.J., Martinez-Ortiz, W.
• Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI), National Institutes of Health/Office of the Director

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Re-refinement Note

This entry reflects an alternative modeling of the original data in: EMD-9513

Literature

An Improved Method for Modeling Voltage-Gated Ion Channels at Atomic Accuracy Applied to Human CavChannels.

Martinez-Ortiz, W., Cardozo, T.J.

(2018) Cell Rep 23: 1399-1408

• PubMed: 29719253 
• DOI: https://doi.org/10.1016/j.celrep.2018.04.024
• Primary Citation of Related Structures:  
  6BYO


• PubMed Abstract: 
  

  Voltage-gated ion channels (VGICs) are associated with hundreds of human diseases. To date, 3D structural models of human VGICs have not been reported. We developed a 3D structural integrity metric to rank the accuracy of all VGIC structures deposited in the PDB. The metric revealed inaccuracies in structural models built from recent single-particle, non-crystalline cryo-electron microscopy maps and enabled the building of highly accurate homology models of human Ca _v channel α ₁ subunits at atomic resolution. Human Ca _v Mendelian mutations mostly located to segments involved in the mechanism of voltage sensing and gating within the 3D structure, with multiple mutations targeting equivalent 3D structural locations despite eliciting distinct clinical phenotypes. The models also revealed that the architecture of the ion selectivity filter is highly conserved from bacteria to humans and between sodium and calcium VGICs.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: homology

Macromolecule Content

• Total Structure Weight: 155.06 kDa 
• Atom Count: 9,158 
• Modelled Residue Count: 1,129 
• Deposited Residue Count: 1,357 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Voltage-dependent L-type calcium channel subunit alpha-1S	A	1,357	Oryctolagus cuniculus	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for P07293 (Oryctolagus cuniculus) Explore P07293  Go to UniProtKB:  P07293

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-05-02 
Deposition Author(s): Cardozo, T.J., Martinez-Ortiz, W.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	5 F31 HL124898 04
National Institutes of Health/Office of the Director	United States	DP2 OD004631

Revision History  

• Version 1.0: 2018-05-02
  Type: Initial release
  
• Version 1.1: 2018-05-16
  Changes: Data collection, Database references
• Version 1.2: 2019-02-20
  Changes: Author supporting evidence, Data collection
• Version 1.3: 2019-04-17
  Changes: Author supporting evidence, Data collection
• Version 1.4: 2019-12-04
  Changes: Author supporting evidence