9OUM | pdb_00009oum

Native GABA-A receptor from rat cerebella, beta2-alpha1-beta1-alpha6-gamma2 subtype, in complex with GABA and PZ-II-029


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9OUM

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Literature

Molecular assemblies and pharmacology of cerebellar GABA A receptors.

Sun, C.Jahncke, J.N.Wright, K.M.Gouaux, E.

(2026) Proc Natl Acad Sci U S A 123: e2524504123-e2524504123

  • DOI: https://doi.org/10.1073/pnas.2524504123
  • Primary Citation Related Structures: 
    9OUM, 9OUN, 9OUO, 9OUP, 9OUQ, 9OUR, 9OV4

  • PubMed Abstract: 

    GABA A receptors (GABA A Rs) mediate fast inhibitory neurotransmission in the brain and are assembled from 19 subunit isoforms into multiple pentameric assemblies. Although α1-containing GABA A Rs are broadly expressed and are pharmacologically important, the molecular diversity of native α1-based assemblies in specific brain regions remains incompletely understood. Here, we use immunofluorescence, mass spectrometry, and cryogenic electron microscopy (cryo-EM) to characterize the spatial distribution, subunit composition, and structural architecture of native α1-containing GABA A Rs in the rat cerebellum. Confocal microscopy reveals robust colocalization of α1 and γ2 subunits across cerebellar layers, including prominent labeling at glomerular synapses. Biochemical purification and proteomic analysis identify a range of α, β, and γ subunits, along with abundant α6 and δ subunits. Using cryo-EM and automated subunit identification, we resolve eight α1-containing receptor assemblies, including the first structure of α6-containing receptors. We further determine the binding mode of the α6-selective pyrazoloquinolinone modulator PZ-II-029 at the α + - interface, showing ligand-induced expansion of the entire extracellular domain (ECD). Together, our study defines the structure and subunit composition of the α1-containing cerebellar GABA A Rs and elaborates the molecular interactions between native receptors and pyrazoloquinolinone, thereby laying the groundwork for brain region and subunit-specific pharmacology.


  • Organizational Affiliation
    • Vollum Institute, Oregon Health and Science University, Portland, OR 97239.

Macromolecule Content 

  • Total Structure Weight: 319.24 kDa 
  • Atom Count: 10,660 
  • Modeled Residue Count: 1,277 
  • Deposited Residue Count: 2,758 
  • Unique protein chains: 7

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Gamma-aminobutyric acid receptor subunit beta-1A [auth B]474Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for P15431 (Rattus norvegicus)
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Go to UniProtKB:  P15431
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15431
Glycosylation
Glycosylation Sites: 2Go to GlyGen: P15431-1
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Gamma-aminobutyric acid receptor subunit gamma-2B [auth D]466Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for P18508 (Rattus norvegicus)
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Go to UniProtKB:  P18508
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18508
Glycosylation
Glycosylation Sites: 2Go to GlyGen: P18508-1
Sequence Annotations
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
8E3 Fab heavy chainC [auth H]223Mus musculusMutation(s): 0 
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
8E3 Fab light chainD [auth L]213Mus musculusMutation(s): 0 
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Gamma-aminobutyric acid receptor subunit alpha-1E [auth A]455Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for P62813 (Rattus norvegicus)
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Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62813
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P62813-1
Sequence Annotations
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Gamma-aminobutyric acid receptor subunit beta-2F [auth E]474Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for P63138 (Rattus norvegicus)
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Go to UniProtKB:  P63138
Entity Groups
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UniProt GroupP63138
Glycosylation
Glycosylation Sites: 2Go to GlyGen: P63138-1
Sequence Annotations
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Gamma-aminobutyric acid receptor subunit alpha-6G [auth C]453Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for P30191 (Rattus norvegicus)
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Go to UniProtKB:  P30191
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP30191
Glycosylation
Glycosylation Sites: 2Go to GlyGen: P30191-1
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 8
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseH [auth F],
J [auth I],
L [auth K],
N
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT
Entity ID: 9
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseI [auth G],
M,
O
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE
Entity ID: 10
MoleculeChains Length2D Diagram GlycosylationD 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-glucopyranoseK [auth J]7N-Glycosylation
Glycosylation Resources
GlyTouCan: G07617FP
GlyCosmos: G07617FP
GlyGen: G07617FP

Small Molecules

Binding Affinity Annotations 
IDSourceBinding Affinity
ABU BindingDB:  9OUM Ki: min: 21.37, max: 77.62 (nM) from 4 assay(s)
EC50: min: 230, max: 8.00e+4 (nM) from 20 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2026-02-18
    Type: Initial release