4COF | pdb_00004cof

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

PDB DOI: https://doi.org/10.2210/pdb4COF/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No
Membrane Protein: Yes OPM PDBTM MemProtMD mpstruc

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.97 Å
R-Value Free:
0.226 (Depositor), 0.235 (DCC)
R-Value Work:
0.205 (Depositor), 0.215 (DCC)
R-Value Observed:
0.206 (Depositor)

Starting Model: experimental
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Literature

Crystal Structure of a Human Gabaa Receptor

Miller, P.S., Aricescu, A.R.

(2014) Nature 512: 270

PubMed: 24909990 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/nature13293
Primary Citation 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.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 209.2 kDa
Atom Count: 13,972
Modeled Residue Count: 1,665
Deposited Residue Count: 1,775
Unique protein chains: 1

Macromolecules

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| 3D Structure

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 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P28472 (Homo sapiens) Explore P28472 Go to UniProtKB: P28472
PHAROS: P28472 GTEx: ENSG00000166206
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P28472
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D Focus chain E	Go to GlyGen: P28472-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
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	Interactions Focus chain F Focus chain G Focus chain H Focus chain I Focus chain J Interactions & Density Focus chain F Focus chain G Focus chain H Focus chain I Focus chain J
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain Z [auth E] SDF format, chain W [auth D] SDF format, chain T [auth C] SDF format, chain Q [auth B] SDF format, chain N [auth A] SDF format, chain L [auth A] MOL2 format, chain Z [auth E] MOL2 format, chain W [auth D] MOL2 format, chain T [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain N [auth A] MOL2 format, chain L [auth A] mmCIF format, chain Z [auth E] mmCIF format, chain W [auth D] mmCIF format, chain T [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain N [auth A] mmCIF format, chain L [auth A]	L [auth A] N [auth A] Q [auth B] T [auth C] W [auth D] L [auth A], N [auth A], Q [auth B], T [auth C], W [auth D], Z [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain L [auth A] Focus chain N [auth A] Focus chain Q [auth B] Focus chain T [auth C] Focus chain W [auth D] Focus chain Z [auth E] Interactions & Density Focus chain L [auth A] Focus chain N [auth A] Focus chain Q [auth B] Focus chain T [auth C] Focus chain W [auth D] Focus chain Z [auth E]
BEN Query on BEN Download:Ideal Coordinates CCD File SDF format, chain X [auth E] SDF format, chain U [auth D] SDF format, chain R [auth C] SDF format, chain O [auth B] SDF format, chain K [auth A] MOL2 format, chain X [auth E] MOL2 format, chain U [auth D] MOL2 format, chain R [auth C] MOL2 format, chain O [auth B] MOL2 format, chain K [auth A] mmCIF format, chain X [auth E] mmCIF format, chain U [auth D] mmCIF format, chain R [auth C] mmCIF format, chain O [auth B] mmCIF format, chain K [auth A]	K [auth A], O [auth B], R [auth C], U [auth D], X [auth E]	BENZAMIDINE C₇ H₈ N₂ PXXJHWLDUBFPOL-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain O [auth B] Focus chain R [auth C] Focus chain U [auth D] Focus chain X [auth E] Interactions & Density Focus chain K [auth A] Focus chain O [auth B] Focus chain R [auth C] Focus chain U [auth D] Focus chain X [auth E]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain Y [auth E] SDF format, chain V [auth D] SDF format, chain S [auth C] SDF format, chain P [auth B] SDF format, chain M [auth A] MOL2 format, chain Y [auth E] MOL2 format, chain V [auth D] MOL2 format, chain S [auth C] MOL2 format, chain P [auth B] MOL2 format, chain M [auth A] mmCIF format, chain Y [auth E] mmCIF format, chain V [auth D] mmCIF format, chain S [auth C] mmCIF format, chain P [auth B] mmCIF format, chain M [auth A]	M [auth A], P [auth B], S [auth C], V [auth D], Y [auth E]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain M [auth A] Focus chain P [auth B] Focus chain S [auth C] Focus chain V [auth D] Focus chain Y [auth E] Interactions & Density Focus chain M [auth A] Focus chain P [auth B] Focus chain S [auth C] Focus chain V [auth D] Focus chain Y [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.97 Å
R-Value Free: 0.226 (Depositor), 0.235 (DCC)
R-Value Work: 0.205 (Depositor), 0.215 (DCC)
R-Value Observed: 0.206 (Depositor)

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

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Entry History

Deposition Data

Released Date: 2014-06-04

Deposition Author(s):

Miller, P.S.

Aricescu, A.R.

Revision History (Full details and data files)

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
Version 2.1: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
Version 2.2: 2024-11-06
Changes: Structure summary