6HUP

CryoEM structure of human full-length alpha1beta3gamma2L GABA(A)R in complex with diazepam (Valium), GABA and megabody Mb38.

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.58 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history. 


Literature

GABAAreceptor signalling mechanisms revealed by structural pharmacology.

Masiulis, S., Desai, R., Uchanski, T., Serna Martin, I., Laverty, D., Karia, D., Malinauskas, T., Zivanov, J., Pardon, E., Kotecha, A., Steyaert, J., Miller, K.W., Aricescu, A.R.

(2019) Nature 565: 454-459

  • DOI: 10.1038/s41586-018-0832-5
  • Primary Citation of Related Structures:  
    6HUK, 6HUP, 6HUO, 6HUG, 6HUJ

  • PubMed Abstract: 

    • Type-A γ-aminobutyric (GABA A ) receptors are ligand-gated chloride channels with a very rich pharmacology. Some of their modulators, including benzodiazepines and general anaesthetics, are among the most successful drugs in clinical use and are common substances of abuse ...

    Type-A γ-aminobutyric (GABA A ) receptors are ligand-gated chloride channels with a very rich pharmacology. Some of their modulators, including benzodiazepines and general anaesthetics, are among the most successful drugs in clinical use and are common substances of abuse. Without reliable structural data, the mechanistic basis for the pharmacological modulation of GABA A receptors remains largely unknown. Here we report several high-resolution cryo-electron microscopy structures in which the full-length human α1β3γ2L GABA A receptor in lipid nanodiscs is bound to the channel-blocker picrotoxin, the competitive antagonist bicuculline, the agonist GABA (γ-aminobutyric acid), and the classical benzodiazepines alprazolam and diazepam. We describe the binding modes and mechanistic effects of these ligands, the closed and desensitized states of the GABA A receptor gating cycle, and the basis for allosteric coupling between the extracellular, agonist-binding region and the transmembrane, pore-forming region. This work provides a structural framework in which to integrate previous physiology and pharmacology research and a rational basis for the development of GABA A receptor modulators.

    Organizational Affiliation: 

    Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK. radu@mrc-lmb.cam.ac.uk.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Gamma-aminobutyric acid receptor subunit alpha-1,Gamma-aminobutyric acid receptor subunit alpha-1 A, D464Bos taurus, Homo sapiens
This entity is chimeric		Mutation(s): 0 
Gene Names: GABRA1
Membrane protein
Mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Cys-Loop Receptor Family		Protein: 
α1β3γ2L GABAA receptor in complex with picrotoxin
Find proteins for P08219 (Bos taurus)
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Go to UniProtKB:  P08219
Find proteins for P14867 (Homo sapiens)
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Go to UniProtKB:  P14867
NIH Common Fund Data Resources
PHAROS:  P14867
GTEx:  ENSG00000022355
Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Gamma-aminobutyric acid receptor subunit beta-3 B, E473Homo sapiensMutation(s): 0 
Gene Names: GABRB3
Membrane protein
Mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Cys-Loop Receptor Family		Protein: 
α1β3γ2L GABAA receptor in complex with picrotoxin
Find proteins for P28472 (Homo sapiens)
Explore P28472 
Go to UniProtKB:  P28472
NIH Common Fund Data Resources
PHAROS:  P28472
GTEx:  ENSG00000166206
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Gamma-aminobutyric acid receptor subunit gamma-2 C495Homo sapiensMutation(s): 0 
Gene Names: GABRG2
Membrane protein
Mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Cys-Loop Receptor Family		Protein: 
α1β3γ2L GABAA receptor in complex with picrotoxin
Find proteins for P18507 (Homo sapiens)
Explore P18507 
Go to UniProtKB:  P18507
NIH Common Fund Data Resources
PHAROS:  P18507
GTEx:  ENSG00000113327
Protein Feature View
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Megabody Mb38 G539Lama glamaMutation(s): 0 
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  • Reference Sequence
Oligosaccharides

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Entity ID: 5
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
F
7 N-Glycosylation Oligosaccharides Interaction
Entity ID: 6
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
H, J, L
2 N-Glycosylation Oligosaccharides Interaction
Entity ID: 7
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
I, M
6 N-Glycosylation Oligosaccharides Interaction
Entity ID: 8
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
K
5 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PIO
Query on PIO
Download Ideal Coordinates CCD File 
A, D
[(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate
C25 H49 O19 P3
XLNCEHRXXWQMPK-MJUMVPIBSA-N		 Ligand Interaction
DZP
Query on DZP
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B, D, E
7-CHLORO-1-METHYL-5-PHENYL-1,3-DIHYDRO-2H-1,4-BENZODIAZEPIN-2-ONE
C16 H13 Cl N2 O
AAOVKJBEBIDNHE-UHFFFAOYSA-N		 Ligand Interaction
ABU
Query on ABU
Download Ideal Coordinates CCD File 
B, E
GAMMA-AMINO-BUTANOIC ACID
C4 H9 N O2
BTCSSZJGUNDROE-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.58 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomMR/L009609/1
Medical Research Council (United Kingdom)United KingdomMC_UP_1201/15
Medical Research Council (United Kingdom)United KingdomMC_UP_A025_1013
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/M024709/1
Cancer Research UKUnited KingdomC20724/A14414
Human Frontier Science ProgramUnited KingdomRGP0065/2014
Swiss National Science FoundationSwitzerland168735
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM 58448

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-02
    Type: Initial release
  • Version 1.1: 2019-01-16
    Changes: Data collection, Database references
  • Version 1.2: 2019-01-23
    Changes: Data collection, Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary