3RIA | pdb_00003ria

C. elegans glutamate-gated chloride channel (GluCl) in complex with Fab, ivermectin and iodide.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 
    0.280 (Depositor), 0.273 (DCC) 
  • R-Value Work: 
    0.266 (Depositor), 0.254 (DCC) 
  • R-Value Observed: 
    0.267 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history

Literature

Principles of activation and permeation in an anion-selective Cys-loop receptor.

Hibbs, R.E.Gouaux, E.

(2011) Nature 474: 54-60

  • DOI: https://doi.org/10.1038/nature10139
  • Primary Citation Related Structures: 
    3RHW, 3RI5, 3RIA, 3RIF

  • PubMed Abstract: 

    Fast inhibitory neurotransmission is essential for nervous system function and is mediated by binding of inhibitory neurotransmitters to receptors of the Cys-loop family embedded in the membranes of neurons. Neurotransmitter binding triggers a conformational change in the receptor, opening an intrinsic chloride channel and thereby dampening neuronal excitability. Here we present the first three-dimensional structure, to our knowledge, of an inhibitory anion-selective Cys-loop receptor, the homopentameric Caenorhabditis elegans glutamate-gated chloride channel α (GluCl), at 3.3 Å resolution. The X-ray structure of the GluCl-Fab complex was determined with the allosteric agonist ivermectin and in additional structures with the endogenous neurotransmitter L-glutamate and the open-channel blocker picrotoxin. Ivermectin, used to treat river blindness, binds in the transmembrane domain of the receptor and stabilizes an open-pore conformation. Glutamate binds in the classical agonist site at subunit interfaces, and picrotoxin directly occludes the pore near its cytosolic base. GluCl provides a framework for understanding mechanisms of fast inhibitory neurotransmission and allosteric modulation of Cys-loop receptors.


  • Organizational Affiliation
    • Vollum Institute, Oregon Health and Science University, 3181 SW Sam Jackson Park Road, Portland, Oregon 97239, USA.

Macromolecule Content 

  • Total Structure Weight: 437.83 kDa 
  • Atom Count: 29,159 
  • Modeled Residue Count: 3,697 
  • Deposited Residue Count: 3,890 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Avermectin-sensitive glutamate-gated chloride channel GluCl alpha
A, B, C, D, E
347Caenorhabditis elegansMutation(s): 0 
Gene Names: glc-1F11A5.10
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Mouse monoclonal Fab fragment, heavy chain
F, G, H, I, J
221Mus musculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Mouse monoclonal Fab fragment, light chain
K, L, M, N, O
210Mus musculusMutation(s): 0 

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IVM

Query on IVM



Download:Ideal Coordinates CCD File
CA [auth E],
DA [auth E],
P [auth A],
Y [auth C],
Z [auth C]
(2aE,4E,5'S,6S,6'R,7S,8E,11R,13R,15S,17aR,20R,20aR,20bS)-6'-[(2S)-butan-2-yl]-20,20b-dihydroxy-5',6,8,19-tetramethyl-17 -oxo-3',4',5',6,6',10,11,14,15,17,17a,20,20a,20b-tetradecahydro-2H,7H-spiro[11,15-methanofuro[4,3,2-pq][2,6]benzodioxacy clooctadecine-13,2'-pyran]-7-yl 2,6-dideoxy-4-O-(2,6-dideoxy-3-O-methyl-alpha-L-arabino-hexopyranosyl)-3-O-methyl-alpha-L-arabino-hexopyranoside
C48 H74 O14
AZSNMRSAGSSBNP-XPNPUAGNSA-N
LMT

Query on LMT



Download:Ideal Coordinates CCD File
Q [auth A],
R [auth A],
T [auth B]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
UND

Query on UND



Download:Ideal Coordinates CCD File
V [auth B]UNDECANE
C11 H24
RSJKGSCJYJTIGS-UHFFFAOYSA-N
IOD

Query on IOD



Download:Ideal Coordinates CCD File
BA [auth D],
FA [auth E],
S [auth A],
W [auth B]
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
OCT

Query on OCT



Download:Ideal Coordinates CCD File
AA [auth D],
EA [auth E],
U [auth B]
N-OCTANE
C8 H18
TVMXDCGIABBOFY-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
X [auth C]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free:  0.280 (Depositor), 0.273 (DCC) 
  • R-Value Work:  0.266 (Depositor), 0.254 (DCC) 
  • R-Value Observed: 0.267 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 155.099α = 90
b = 155.099β = 90
c = 578.257γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-05-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-10-19
    Changes: Database references
  • Version 1.3: 2017-08-23
    Changes: Refinement description, Source and taxonomy
  • Version 1.4: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 1.5: 2024-11-27
    Changes: Structure summary