4TNW

C. elegans glutamate-gated chloride channel (GluCl) in complex with Fab and POPC in a lipid-modulated conformation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

X-ray structures of GluCl in apo states reveal a gating mechanism of Cys-loop receptors.

Althoff, T.Hibbs, R.E.Banerjee, S.Gouaux, E.

(2014) Nature 512: 333-337

  • DOI: 10.1038/nature13669
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Cys-loop receptors are neurotransmitter-gated ion channels that are essential mediators of fast chemical neurotransmission and are associated with a large number of neurological diseases and disorders, as well as parasitic infections. Members of this ...

    Cys-loop receptors are neurotransmitter-gated ion channels that are essential mediators of fast chemical neurotransmission and are associated with a large number of neurological diseases and disorders, as well as parasitic infections. Members of this ion channel superfamily mediate excitatory or inhibitory neurotransmission depending on their ligand and ion selectivity. Structural information for Cys-loop receptors comes from several sources including electron microscopic studies of the nicotinic acetylcholine receptor, high-resolution X-ray structures of extracellular domains and X-ray structures of bacterial orthologues. In 2011 our group published structures of the Caenorhabditis elegans glutamate-gated chloride channel (GluCl) in complex with the allosteric partial agonist ivermectin, which provided insights into the structure of a possibly open state of a eukaryotic Cys-loop receptor, the basis for anion selectivity and channel block, and the mechanism by which ivermectin and related molecules stabilize the open state and potentiate neurotransmitter binding. However, there remain unanswered questions about the mechanism of channel opening and closing, the location and nature of the shut ion channel gate, the transitions between the closed/resting, open/activated and closed/desensitized states, and the mechanism by which conformational changes are coupled between the extracellular, orthosteric agonist binding domain and the transmembrane, ion channel domain. Here we present two conformationally distinct structures of C. elegans GluCl in the absence of ivermectin. Structural comparisons reveal a quaternary activation mechanism arising from rigid-body movements between the extracellular and transmembrane domains and a mechanism for modulation of the receptor by phospholipids.


    Related Citations: 
    • Principles of activation and permeation in an anion-selective Cys-loop receptor.
      Hibbs, R.E.,Gouaux, E.
      (2011) Nature 474: 54


    Organizational Affiliation

    1] Vollum Institute, Oregon Health &Science University, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239, USA [2] Department of Physiology, David Geffen School of Medicine, University of California Los Angeles, 10833 Le Conte Avenue, Los Angeles, California 90095-1751, USA (T.A.); Department of Neuroscience, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, Texas 75390-9111, USA (R.E.H.). [3].,1] Vollum Institute, Oregon Health &Science University, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239, USA [2] Howard Hughes Medical Institute, Oregon Health &Science University, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239, USA.,NE-CAT/Cornell University, 9700 South Cass Avenue, Building 436 E001, Argonne, Illinois 60439, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Avermectin-sensitive glutamate-gated chloride channel GluCl alpha
A, B, C, D, E, P, Q, R, S, T
347Caenorhabditis elegansMutation(s): 0 
Gene Names: glc-1
Find proteins for G5EBR3 (Caenorhabditis elegans)
Go to UniProtKB:  G5EBR3
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Mouse monoclonal Fab fragment, heavy chain
F, G, H, I, U, V, W, X, Y, J
224N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Mouse monoclonal Fab fragment, light chain
K, L, N, O, Z, f, g, h, i, M
215N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, P
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
LMT
Query on LMT

Download SDF File 
Download CCD File 
B, C, D, E, P, S, T
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C, D, E, P, Q, S, T
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
POV
Query on POV

Download SDF File 
Download CCD File 
A, D, P, Q, R, T
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
POPC
C42 H82 N O8 P
WTJKGGKOPKCXLL-PFDVCBLKSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.227 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 453.750α = 90.00
b = 192.870β = 92.27
c = 196.140γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
Cootmodel building
XSCALEdata scaling
DMphasing
PHASERphasing
HKL-2000data scaling
PHENIXrefinement
XDSdata reduction
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited States5 R01 GM100400
German Research FoundationGermanyAL 1725-1/1
National Institutes of Health/National Institute of Neurological Disorders and StrokeUnited StatesF32NS061404

Revision History 

  • Version 1.0: 2014-08-13
    Type: Initial release
  • Version 1.1: 2014-09-03
    Type: Database references
  • Version 1.2: 2017-09-27
    Type: Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy, Structure summary