4P9O

Complex of Voltage-gated ion channel in a the presence of channel blocking compound

• PDB DOI:  https://doi.org/10.2210/pdb4P9O/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Magnetococcus marinus MC-1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-04-04 Released: 2014-06-04 
• Deposition Author(s): Naylor, C.E., Bagneris, C., Wallace, B.A.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.89 Å
• R-Value Free: 0.251 
• R-Value Work: 0.214 
• R-Value Observed: 0.216 

Literature

Prokaryotic NavMs channel as a structural and functional model for eukaryotic sodium channel antagonism.

Bagneris, C., DeCaen, P.G., Naylor, C.E., Pryde, D.C., Nobeli, I., Clapham, D.E., Wallace, B.A.

(2014) Proc Natl Acad Sci U S A 111: 8428-8433

• PubMed: 24850863 
• DOI: https://doi.org/10.1073/pnas.1406855111
• Primary Citation of Related Structures:  
  4CBC, 4OXS, 4P2Z, 4P30, 4P9O, 4P9P, 4PA3, 4PA4, 4PA6, 4PA7, 4PA9


• PubMed Abstract: 
  

Voltage-gated sodium channels are important targets for the development of pharmaceutical drugs, because mutations in different human sodium channel isoforms have causal relationships with a range of neurological and cardiovascular diseases. In this study, functional electrophysiological studies show that the prokaryotic sodium channel from Magnetococcus marinus (NavMs) binds and is inhibited by eukaryotic sodium channel blockers in a manner similar to the human Nav1.1 channel, despite millions of years of divergent evolution between the two types of channels. Crystal complexes of the NavMs pore with several brominated blocker compounds depict a common antagonist binding site in the cavity, adjacent to lipid-facing fenestrations proposed to be the portals for drug entry. In silico docking studies indicate the full extent of the blocker binding site, and electrophysiology studies of NavMs channels with mutations at adjacent residues validate the location. These results suggest that the NavMs channel can be a valuable tool for screening and rational design of human drugs.

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Related Citations: 

• Role of the C-terminal domain in the structure and function of tetrameric sodium channels.
  Bagneris, C., Decaen, P.G., Hall, B.A., Naylor, C.E., Clapham, D.E., Kay, C.W., Wallace, B.A.
  (2013) Nat Commun 4: 2465

• Structure of a bacterial voltage-gated sodium channel pore reveals mechanisms of opening and closing.
  McCusker, E.C., Bagneris, C., Naylor, C.E., Cole, A.R., D'Avanzo, N., Nichols, C.G., Wallace, B.A.
  (2012) Nat Commun 3: 1102

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Organizational Affiliation: 

Institute of Structural and Molecular Biology, School of Biological Sciences, Birkbeck College, University of London, London WC1E 7HX, United Kingdom; [e-mail] [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C4  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 69.94 kDa 
• Atom Count: 3,232 
• Modelled Residue Count: 364 
• Deposited Residue Count: 596 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ion transport protein	A, B, C, D	149	Magnetococcus marinus MC-1	Mutation(s): 0  Gene Names: Mmc1_0798

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2CV	E [auth A], F [auth A], H [auth B], I [auth B], K [auth C], M [auth D]	HEGA-10 C18 H37 N O7 ITEIKACYSCODFV-ATLSCFEFSA-N
BR	G [auth B], J [auth B], L [auth D], N [auth D]	BROMIDE ION Br CPELXLSAUQHCOX-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.89 Å
• R-Value Free: 0.251 
• R-Value Work: 0.214 
• R-Value Observed: 0.216 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.42	α = 90
b = 328.37	β = 90
c = 80.39	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2014-06-04 
Deposition Author(s): Naylor, C.E., Bagneris, C., Wallace, B.A.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/H02070X
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/J020702

Revision History  

• Version 1.0: 2014-06-04
  Type: Initial release
  
• Version 1.1: 2014-08-06
  Changes: Database references
• Version 2.0: 2017-09-20
  Changes: Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Other, Source and taxonomy, Structure summary
• Version 2.1: 2020-01-01
  Changes: Author supporting evidence