4MS4

Crystal structure of the extracellular domain of human GABA(B) receptor bound to the agonist baclofen


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.3 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
  • Structures With Same Primary Citation

  • 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

    1] Department of Pharmacology, Columbia University, New York, New York 10032, USA [2] Department of Pathology & Cell Biology, Columbia University, New York, New York 10032, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Gamma-aminobutyric acid type B receptor subunit 2B433Homo sapiensMutation(s): 0 
Gene Names: GABBR2GPR51GPRC3B
Membrane protein
Mpstruc
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)
Explore O75899 
Go to UniProtKB:  O75899
NIH Common Fund Data Resources
PHAROS  O75899
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Gamma-aminobutyric acid type B receptor subunit 1A420Homo sapiensMutation(s): 0 
Gene Names: GABBR1GPRC3A
Membrane protein
Mpstruc
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)
Explore Q9UBS5 
Go to UniProtKB:  Q9UBS5
NIH Common Fund Data Resources
PHAROS  Q9UBS5
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
B
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
2C0
Query on 2C0

Download CCD File 
A
baclofen
C10 H12 Cl N O2
KPYSYYIEGFHWSV-QMMMGPOBSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
2C0IC50:  330   nM  BindingDB
2C0IC50:  140   nM  BindingDB
2C0EC50:  1700   nM  BindingDB
2C0IC50:  32   nM  BindingDB
2C0IC50:  30   nM  BindingDB
2C0IC50:  35   nM  BindingDB
2C0IC50:  107   nM  BindingDB
2C0IC50:  420   nM  BindingDB
2C0IC50:  200   nM  BindingDB
2C0IC50:  180   nM  BindingDB
2C0EC50:  1000   nM  BindingDB
2C0EC50:  750   nM  BindingDB
2C0Ki:  220   nM  BindingDB
2C0Ki:  6000   nM  BindingDB
2C0IC50:  60   nM  BindingDB
2C0IC50:  15   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 
  • Space Group: P 21 21 2
  • Diffraction Data DOI: 10.15785/SBGRID/58 SBGrid
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.383α = 90
b = 140.39β = 90
c = 59.501γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
DENZOdata reduction
PHASERphasing
BUSTERrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-12-11
    Type: Initial release
  • Version 1.1: 2013-12-18
    Changes: Database references
  • Version 1.2: 2014-02-05
    Changes: Database references
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary