5CFB

Crystal Structure of Human Glycine Receptor alpha-3 Bound to Strychnine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.04 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.260 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Crystal structure of human glycine receptor-alpha 3 bound to antagonist strychnine.

Huang, X.Chen, H.Michelsen, K.Schneider, S.Shaffer, P.L.

(2015) Nature 526: 277-280

  • DOI: 10.1038/nature14972

  • PubMed Abstract: 
  • Neurotransmitter-gated ion channels of the Cys-loop receptor family are essential mediators of fast neurotransmission throughout the nervous system and are implicated in many neurological disorders. Available X-ray structures of prokaryotic and eukar ...

    Neurotransmitter-gated ion channels of the Cys-loop receptor family are essential mediators of fast neurotransmission throughout the nervous system and are implicated in many neurological disorders. Available X-ray structures of prokaryotic and eukaryotic Cys-loop receptors provide tremendous insights into the binding of agonists, the subsequent opening of the ion channel, and the mechanism of channel activation. Yet the mechanism of inactivation by antagonists remains unknown. Here we present a 3.0 Å X-ray structure of the human glycine receptor-α3 homopentamer in complex with a high affinity, high-specificity antagonist, strychnine. Our structure allows us to explore in detail the molecular recognition of antagonists. Comparisons with previous structures reveal a mechanism for antagonist-induced inactivation of Cys-loop receptors, involving an expansion of the orthosteric binding site in the extracellular domain that is coupled to closure of the ion pore in the transmembrane domain.


    Organizational Affiliation

    Department of Molecular Structure and Characterization, Amgen Inc., 360 Binney Street, Cambridge, Massachusetts 02142, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glycine receptor subunit alpha-3,Glycine receptor subunit alpha-3
A, B, C, D, E
362Homo sapiensMutation(s): 0 
Gene Names: GLRA3
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Cys-Loop Receptor Family
Protein: 
Human glycine receptor (hGlyR-α3) in complex with strychnine
Find proteins for O75311 (Homo sapiens)
Go to Gene View: GLRA3
Go to UniProtKB:  O75311
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SY9
Query on SY9

Download SDF File 
Download CCD File 
A, B, C, D, E
STRYCHNINE
C21 H22 N2 O2
QMGVPVSNSZLJIA-FVWCLLPLSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C, D, E
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.04 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.260 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 140.242α = 90.00
b = 143.198β = 90.00
c = 180.054γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHASERphasing
SCALEPACKdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-09-30
    Type: Initial release
  • Version 1.1: 2015-10-14
    Type: Database references
  • Version 1.2: 2015-10-21
    Type: Database references
  • Version 1.3: 2016-07-20
    Type: Data collection
  • Version 1.4: 2017-11-22
    Type: Derived calculations, Refinement description