9CSB

Native human GABAA receptor of beta3-alpha1-beta2-alpha2-gamma2 assembly


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.34 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Resolving native GABA A receptor structures from the human brain.

Zhou, J.Noviello, C.M.Teng, J.Moore, H.Lega, B.Hibbs, R.E.

(2025) Nature 

  • DOI: https://doi.org/10.1038/s41586-024-08454-1
  • Primary Citation of Related Structures:  
    9CRS, 9CRV, 9CSB, 9CT0, 9CTJ, 9CTP, 9CTV, 9CX7, 9CXA, 9CXB, 9CXC, 9CXD, 9DRX

  • PubMed Abstract: 

    Type A GABA (γ-aminobutyric acid) receptors (GABA A receptors) mediate most fast inhibitory signalling in the brain and are targets for drugs that treat epilepsy, anxiety, depression and insomnia and for anaesthetics 1,2 . These receptors comprise a complex array of 19 related subunits, which form pentameric ligand-gated ion channels. The composition and structure of native GABA A receptors in the human brain have been inferred from subunit localization in tissue 1,3 , functional measurements and structural analysis from recombinant expression 4-7 and in mice 8 . However, the arrangements of subunits that co-assemble physiologically in native human GABA A receptors remain unknown. Here we isolated α1 subunit-containing GABA A receptors from human patients with epilepsy. Using cryo-electron microscopy, we defined a set of 12 native subunit assemblies and their 3D structures. We address inconsistencies between previous native and recombinant approaches, and reveal details of previously undefined subunit interfaces. Drug-like densities in a subset of these interfaces led us to uncover unexpected activity on the GABA A receptor of antiepileptic drugs and resulted in localization of one of these drugs to the benzodiazepine-binding site. Proteomics and further structural analysis suggest interactions with the auxiliary subunits neuroligin 2 and GARLH4, which localize and modulate GABA A receptors at inhibitory synapses. This work provides a structural foundation for understanding GABA A receptor signalling and targeted pharmacology in the human brain.


  • Organizational Affiliation

    Department of Neurobiology, University of California San Diego, La Jolla, CA, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Gamma-aminobutyric acid receptor subunit beta-3448Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P28472 (Homo sapiens)
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PHAROS:  P28472
GTEx:  ENSG00000166206 
Entity Groups  
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UniProt GroupP28472
Glycosylation
Glycosylation Sites: 2Go to GlyGen: P28472-1
Sequence Annotations
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Gamma-aminobutyric acid receptor subunit alpha-1429Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P14867 (Homo sapiens)
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PHAROS:  P14867
GTEx:  ENSG00000022355 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14867
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P14867-1
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Gamma-aminobutyric acid receptor subunit beta-2488Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P47870 (Homo sapiens)
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PHAROS:  P47870
GTEx:  ENSG00000145864 
Entity Groups  
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UniProt GroupP47870
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P47870-2
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Gamma-aminobutyric acid receptor subunit alpha-2423Homo sapiensMutation(s): 0 
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Find proteins for P47869 (Homo sapiens)
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PHAROS:  P47869
GTEx:  ENSG00000151834 
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UniProt GroupP47869
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Gamma-aminobutyric acid receptor subunit gamma-2436Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P18507 (Homo sapiens)
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PHAROS:  P18507
GTEx:  ENSG00000113327 
Entity Groups  
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UniProt GroupP18507
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P18507-2
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Kappa Fab_1F4 Light ChainF [auth I]213Mus musculusMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
IgG2b Fab_1F4 Heavy ChainG [auth J]454Mus musculusMutation(s): 0 
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Oligosaccharides

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Entity ID: 8
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseH [auth F],
J [auth H]
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 9
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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-glucopyranoseI [auth G]7N-Glycosylation
Glycosylation Resources
GlyTouCan:  G07617FP
GlyCosmos:  G07617FP
GlyGen:  G07617FP
Entity ID: 10
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseK [auth O]2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
POV (Subject of Investigation/LOI)
Query on POV

Download Ideal Coordinates CCD File 
M [auth B](2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
C42 H82 N O8 P
WTJKGGKOPKCXLL-PFDVCBLKSA-N
PIO (Subject of Investigation/LOI)
Query on PIO

Download Ideal Coordinates CCD File 
L [auth B],
N [auth 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
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
O [auth E]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.34 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
American Heart AssociationUnited States24POST1195454
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)United StatesDA047325

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-22
    Type: Initial release
  • Version 1.1: 2025-02-05
    Changes: Data collection, Database references