Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C5  (3D View)
Global Stoichiometry: Homo 5-mer - A5 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 209.20 kDa 
• Atom Count: 13972 
• Residue Count: 1665 
• Unique protein chains: 1

4COF

Crystal structure of a human gamma-aminobutyric acid receptor, the GABA(A)R-beta3 homopentamer

• DOI: 10.2210/pdb4COF/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2014-01-28 Released: 2014-06-04 
• Deposition Author(s): Miller, P.S., Aricescu, A.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.97 Å
• R-Value Free: 0.226 
• R-Value Work: 0.205 
• R-Value Observed: 0.206 

Literature

Crystal Structure of a Human Gabaa Receptor

Miller, P.S., Aricescu, A.R.

(2014) Nature 512: 270

• PubMed: 24909990 
• DOI: 10.1038/nature13293
• Primary Citation of Related Structures:  
  4COF


• PubMed Abstract: 
  

Type-A γ-aminobutyric acid receptors (GABAARs) are the principal mediators of rapid inhibitory synaptic transmission in the human brain. A decline in GABAAR signalling triggers hyperactive neurological disorders such as insomnia, anxiety and epilepsy. Here we present the first three-dimensional structure of a GABAAR, the human β3 homopentamer, at 3 Å resolution. This structure reveals architectural elements unique to eukaryotic Cys-loop receptors, explains the mechanistic consequences of multiple human disease mutations and shows an unexpected structural role for a conserved N-linked glycan. The receptor was crystallized bound to a previously unknown agonist, benzamidine, opening a new avenue for the rational design of GABAAR modulators. The channel region forms a closed gate at the base of the pore, representative of a desensitized state. These results offer new insights into the signalling mechanisms of pentameric ligand-gated ion channels and enhance current understanding of GABAergic neurotransmission.

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Organizational Affiliation: 

Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GAMMA-AMINOBUTYRIC ACID RECEPTOR SUBUNIT BETA-3	A, B, C, D, E	355	Homo sapiens	Mutation(s): 0  Gene Names: GABRB3
Membrane protein Mpstruc	Group:  TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group:  Cys-Loop Receptor Family	Protein:  GABAA receptor (β3 homopentamer)
Find proteins for P28472 (Homo sapiens) Explore P28472  Go to UniProtKB:  P28472
NIH Common Fund Data Resources
PHAROS  P28472 GTEx  ENSG00000166206

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F, G, H, I, J	3		N-Glycosylation

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	A, B, C, D, E	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
BEN	A, B, C, D, E	BENZAMIDINE C7 H8 N2 PXXJHWLDUBFPOL-UHFFFAOYSA-N
CL	A, B, C, D, E	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.97 Å
• R-Value Free: 0.226 
• R-Value Work: 0.205 
• R-Value Observed: 0.206 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 174.1	α = 90
b = 108.9	β = 107.43
c = 207.44	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-01-28 
• Released Date: 2014-06-04 
Deposition Author(s): Miller, P.S., Aricescu, A.R.

Revision History 

• Version 1.0: 2014-06-04
  Type: Initial release
  
• Version 1.1: 2014-06-11
  Changes: Structure summary
• Version 1.2: 2014-06-18
  Changes: Database references
• Version 1.3: 2014-08-27
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary