4MRM

Crystal structure of the extracellular domain of human GABA(B) receptor bound to the antagonist phaclofen


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.86 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural mechanism of ligand activation in human GABA(B) receptor.

Geng, Y.Bush, M.Mosyak, L.Wang, F.Fan, Q.R.

(2013) Nature 504: 254-259

  • DOI: 10.1038/nature12725
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Human GABA(B) (γ-aminobutyric acid class B) receptor is a G-protein-coupled receptor central to inhibitory neurotransmission in the brain. It functions as an obligatory heterodimer of the subunits GBR1 and GBR2. Here we present the crystal structures ...

    Human GABA(B) (γ-aminobutyric acid class B) receptor is a G-protein-coupled receptor central to inhibitory neurotransmission in the brain. It functions as an obligatory heterodimer of the subunits GBR1 and GBR2. Here we present the crystal structures of a heterodimeric complex between the extracellular domains of GBR1 and GBR2 in the apo, agonist-bound and antagonist-bound forms. The apo and antagonist-bound structures represent the resting state of the receptor; the agonist-bound complex corresponds to the active state. Both subunits adopt an open conformation at rest, and only GBR1 closes on agonist-induced receptor activation. The agonists and antagonists are anchored in the interdomain crevice of GBR1 by an overlapping set of residues. An antagonist confines GBR1 to the open conformation of the inactive state, whereas an agonist induces its domain closure for activation. Our data reveal a unique activation mechanism for GABA(B) receptor that involves the formation of a novel heterodimer interface between subunits.


    Organizational Affiliation

    Department of Pharmacology, Columbia University, New York, New York 10032, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Gamma-aminobutyric acid type B receptor subunit 1
A
420Homo sapiensMutation(s): 0 
Gene Names: GABBR1 (GPRC3A)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs)
Protein: 
GABAB receptor ectodomain GBR1-GBR2 heterodimer, apo form
Find proteins for Q9UBS5 (Homo sapiens)
Go to Gene View: GABBR1
Go to UniProtKB:  Q9UBS5
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Gamma-aminobutyric acid type B receptor subunit 2
B
433Homo sapiensMutation(s): 0 
Gene Names: GABBR2 (GPR51, GPRC3B)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs)
Protein: 
GABAB receptor ectodomain GBR1-GBR2 heterodimer, apo form
Find proteins for O75899 (Homo sapiens)
Go to Gene View: GABBR2
Go to UniProtKB:  O75899
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

Download SDF File 
Download CCD File 
A
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
A
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
2BY
Query on 2BY

Download SDF File 
Download CCD File 
A
phaclofen
[(2R)-3-amino-2-(4-chlorophenyl)propyl]phosphonic acid
C9 H13 Cl N O3 P
VSGNGLJPOGUDON-MRVPVSSYSA-N
 Ligand Interaction
NAG
Query on NAG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.86 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.208 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 70.070α = 90.00
b = 111.940β = 97.67
c = 73.470γ = 90.00
Software Package:
Software NamePurpose
BUSTER-TNTrefinement
DENZOdata reduction
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
HKL-2000data collection
BUSTERrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-12-11
    Type: Initial release
  • Version 1.1: 2013-12-18
    Type: Database references
  • Version 1.2: 2014-02-05
    Type: Database references