2VL0 | pdb_00002vl0

X-ray structure of a pentameric ligand gated ion channel from Erwinia chrysanthemi (ELIC)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 
    0.274 (Depositor), 0.275 (DCC) 
  • R-Value Work: 
    0.263 (Depositor), 0.262 (DCC) 
  • R-Value Observed: 
    0.263 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 2VL0

This is version 1.4 of the entry. See complete history

Literature

X-Ray Structure of a Prokaryotic Pentameric Ligand-Gated Ion Channel

Hilf, R.J.C.Dutzler, R.

(2008) Nature 452: 375

  • DOI: https://doi.org/10.1038/nature06717
  • Primary Citation Related Structures: 
    2VL0

  • PubMed Abstract: 

    Pentameric ligand-gated ion channels (pLGICs) are key players in the early events of electrical signal transduction at chemical synapses. The family codes for a structurally conserved scaffold of channel proteins that open in response to the binding of neurotransmitter molecules. All proteins share a pentameric organization of identical or related subunits that consist of an extracellular ligand-binding domain followed by a transmembrane channel domain. The nicotinic acetylcholine receptor (nAChR) is the most thoroughly studied member of the pLGIC family (for recent reviews see refs 1-3). Two sources of structural information provided an architectural framework for the family. The structure of the soluble acetylcholine-binding protein (AChBP) defined the organization of the extracellular domain and revealed the chemical basis of ligand interaction. Electron microscopy studies of the nAChR from Torpedo electric ray have yielded a picture of the full-length protein and have recently led to the interpretation of an electron density map at 4.0 A resolution. Despite the wealth of experimental information, high-resolution structures of any family member have so far not been available. Until recently, the pLGICs were believed to be only expressed in multicellular eukaryotic organisms. The abundance of prokaryotic genome sequences, however, allowed the identification of several homologous proteins in bacterial sources. Here we present the X-ray structure of a prokaryotic pLGIC from the bacterium Erwinia chrysanthemi (ELIC) at 3.3 A resolution. Our study reveals the first structure of a pLGIC at high resolution and provides an important model system for the investigation of the general mechanisms of ion permeation and gating within the family.


  • Organizational Affiliation
    • Department of Biochemistry, University of Zürich, Winterthurer Strasse 190, CH-8057 Zürich, Switzerland.

Macromolecule Content 

  • Total Structure Weight: 368.22 kDa 
  • Atom Count: 25,010 
  • Modeled Residue Count: 3,060 
  • Deposited Residue Count: 3,210 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cys-loop ligand-gated ion channel
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J
321Dickeya chrysanthemiMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0C7B7 (Dickeya chrysanthemi)
Explore P0C7B7 
Go to UniProtKB:  P0C7B7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C7B7
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free:  0.274 (Depositor), 0.275 (DCC) 
  • R-Value Work:  0.263 (Depositor), 0.262 (DCC) 
  • R-Value Observed: 0.263 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.502α = 90
b = 266.147β = 109.52
c = 110.851γ = 90
Software Package:
Software NamePurpose
CNSrefinement
XDSdata reduction
XSCALEdata scaling
SHELXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-03-11
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-10-09
    Changes: Data collection, Database references, Other, Source and taxonomy, Structure summary
  • Version 1.4: 2024-05-08
    Changes: Data collection, Database references