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- EMDB-70873: Native GABA-A receptor from rat cerebella, beta2-alpha1-beta2-alp... -

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Entry
Database: EMDB / ID: EMD-70873
TitleNative GABA-A receptor from rat cerebella, beta2-alpha1-beta2-alpha1-gamma2 subtype, in complex with GABA and PZ-II-029
Map data
Sample
  • Complex: Native GABA-A receptor from rat cerebella, beta2-alpha1-beta2-alpha1-gamma2 subtype, in complex with GABA and PZ-II-029
    • Protein or peptide: Gamma-aminobutyric acid receptor subunit gamma-2
    • Protein or peptide: 8E3 Fab heavy chain
    • Protein or peptide: 8E3 Fab light chain
    • Protein or peptide: Gamma-aminobutyric acid receptor subunit alpha-1
    • Protein or peptide: Gamma-aminobutyric acid receptor subunit beta-2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: GAMMA-AMINO-BUTANOIC ACID
  • Ligand: 7-methoxy-2-(4-methoxyphenyl)-1,2-dihydro-3H-pyrazolo[4,3-c]quinolin-3-one
Keywordsneurotransmitter receptor / cys-loop receptor / ligand-gated ion channel / MEMBRANE PROTEIN
Function / homology
Function and homology information


diazepam binding / inhibitory extracellular ligand-gated monoatomic ion channel activity / GABA receptor activation / response to methamphetamine hydrochloride / inhibitory synapse / response to auditory stimulus / GABA receptor complex / cellular response to histamine / inner ear receptor cell development / inhibitory synapse assembly ...diazepam binding / inhibitory extracellular ligand-gated monoatomic ion channel activity / GABA receptor activation / response to methamphetamine hydrochloride / inhibitory synapse / response to auditory stimulus / GABA receptor complex / cellular response to histamine / inner ear receptor cell development / inhibitory synapse assembly / GABA-gated chloride ion channel activity / GABA-A receptor complex / GABA-A receptor activity / innervation / chloride transport / response to anesthetic / postsynaptic specialization membrane / gamma-aminobutyric acid signaling pathway / synaptic transmission, GABAergic / adult behavior / cellular response to zinc ion / chloride channel activity / cochlea development / chloride channel complex / neuron development / presynaptic active zone membrane / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / chloride transmembrane transport / cytoplasmic vesicle membrane / post-embryonic development / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / GABA-ergic synapse / dendritic spine / response to ethanol / chemical synaptic transmission / postsynaptic membrane / postsynapse / axon / glutamatergic synapse / cell surface / plasma membrane
Similarity search - Function
Gamma-aminobutyric-acid A receptor, gamma 2 subunit / Gamma-aminobutyric acid receptor subunit gamma-1/4 / Gamma-aminobutyric-acid A receptor, alpha 1 subunit / : / Gamma-aminobutyric-acid A receptor, alpha subunit / : / Gamma-aminobutyric-acid A receptor, beta subunit / Gamma-aminobutyric acid A receptor/Glycine receptor alpha / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. ...Gamma-aminobutyric-acid A receptor, gamma 2 subunit / Gamma-aminobutyric acid receptor subunit gamma-1/4 / Gamma-aminobutyric-acid A receptor, alpha 1 subunit / : / Gamma-aminobutyric-acid A receptor, alpha subunit / : / Gamma-aminobutyric-acid A receptor, beta subunit / Gamma-aminobutyric acid A receptor/Glycine receptor alpha / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. / Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / Neurotransmitter-gated ion-channel transmembrane domain superfamily / Neuronal acetylcholine receptor / Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel ligand-binding domain superfamily / Neurotransmitter-gated ion-channel ligand binding domain
Similarity search - Domain/homology
Gamma-aminobutyric acid receptor subunit gamma-2 / Gamma-aminobutyric acid receptor subunit alpha-1 / Gamma-aminobutyric acid receptor subunit beta-2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.74 Å
AuthorsSun C / Gouaux E
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2026
Title: Molecular assemblies and pharmacology of cerebellar GABA receptors.
Authors: Chang Sun / Jennifer N Jahncke / Kevin M Wright / Eric Gouaux /
Abstract: GABA receptors (GABARs) mediate fast inhibitory neurotransmission in the brain and are assembled from 19 subunit isoforms into multiple pentameric assemblies. Although α1-containing GABARs are ...GABA receptors (GABARs) mediate fast inhibitory neurotransmission in the brain and are assembled from 19 subunit isoforms into multiple pentameric assemblies. Although α1-containing GABARs 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 GABARs 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/γ 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 GABARs and elaborates the molecular interactions between native receptors and pyrazoloquinolinone, thereby laying the groundwork for brain region and subunit-specific pharmacology.
History
DepositionMay 29, 2025-
Header (metadata) releaseFeb 18, 2026-
Map releaseFeb 18, 2026-
UpdateFeb 18, 2026-
Current statusFeb 18, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70873.png

Downloads & links

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Map

FileDownload / File: emd_70873.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
0.96 Å/pix.
x 360 pix.
= 344.16 Å		0.96 Å/pix.
x 360 pix.
= 344.16 Å		0.96 Å/pix.
x 360 pix.
= 344.16 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.956 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.4382655 - 0.87748486
Average (Standard dev.)0.00050402706 (±0.01825386)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 344.16 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: map sharpened with EMReady

Fileemd_70873_additional_1.map
Annotationmap sharpened with EMReady
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_70873_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_70873_half_map_2.map
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Sample components

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Entire : Native GABA-A receptor from rat cerebella, beta2-alpha1-beta2-alp...

EntireName: Native GABA-A receptor from rat cerebella, beta2-alpha1-beta2-alpha1-gamma2 subtype, in complex with GABA and PZ-II-029
Components
  • Complex: Native GABA-A receptor from rat cerebella, beta2-alpha1-beta2-alpha1-gamma2 subtype, in complex with GABA and PZ-II-029
    • Protein or peptide: Gamma-aminobutyric acid receptor subunit gamma-2
    • Protein or peptide: 8E3 Fab heavy chain
    • Protein or peptide: 8E3 Fab light chain
    • Protein or peptide: Gamma-aminobutyric acid receptor subunit alpha-1
    • Protein or peptide: Gamma-aminobutyric acid receptor subunit beta-2
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: GAMMA-AMINO-BUTANOIC ACID
  • Ligand: 7-methoxy-2-(4-methoxyphenyl)-1,2-dihydro-3H-pyrazolo[4,3-c]quinolin-3-one

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Supramolecule #1: Native GABA-A receptor from rat cerebella, beta2-alpha1-beta2-alp...

SupramoleculeName: Native GABA-A receptor from rat cerebella, beta2-alpha1-beta2-alpha1-gamma2 subtype, in complex with GABA and PZ-II-029
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 350 KDa

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Macromolecule #1: Gamma-aminobutyric acid receptor subunit gamma-2

MacromoleculeName: Gamma-aminobutyric acid receptor subunit gamma-2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 54.136945 KDa
SequenceString: MSSPNTWSTG STVYSPVFSQ KMTLWILLLL SLYPGFTSQK SDDDYEDYAS NKTWVLTPKV PEGDVTVILN NLLEGYDNKL RPDIGVKPT LIHTDMYVNS IGPVNAINME YTIDIFFAQT WYDRRLKFNS TIKVLRLNSN MVGKIWIPDT FFRNSKKADA H WITTPNRM ...String:
MSSPNTWSTG STVYSPVFSQ KMTLWILLLL SLYPGFTSQK SDDDYEDYAS NKTWVLTPKV PEGDVTVILN NLLEGYDNKL RPDIGVKPT LIHTDMYVNS IGPVNAINME YTIDIFFAQT WYDRRLKFNS TIKVLRLNSN MVGKIWIPDT FFRNSKKADA H WITTPNRM LRIWNDGRVL YTLRLTIDAE CQLQLHNFPM DEHSCPLEFS SYGYPREEIV YQWKRSSVEV GDTRSWRLYQ FS FVGLRNT TEVVKTTSGD YVVMSVYFDL SRRMGYFTIQ TYIPCTLIVV LSWVSFWINK DAVPARTSLG ITTVLTMTTL STI ARKSLP KVSYVTAMDL FVSVCFIFVF SALVEYGTLH YFVSNRKPSK DKDKKKKNPA PTIDIRPRSA TIQMNNATHL QERD EEYGY ECLDGKDCAS FFCCFEDCRT GAWRHGRIHI RIAKMDSYAR IFFPTAFCLF NLVYWVSYLY L

UniProtKB: Gamma-aminobutyric acid receptor subunit gamma-2

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Macromolecule #2: 8E3 Fab heavy chain

MacromoleculeName: 8E3 Fab heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 24.159895 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: EIQLQQSGPE LVKPGTSVKV SCKASGYSFT DYNMYWVKQS HGKSLEWIGY IDPYNADTTY NREFKGKATL TVDKSSSTAF MHLNSLTSE DSAVYYCARK RNNFYFDYWG QGTPLTVSSA KTTPPSVYPL APGCGDTTGS SVTLGCLVKG YFPESVTVTW N SGSLSSSV ...String:
EIQLQQSGPE LVKPGTSVKV SCKASGYSFT DYNMYWVKQS HGKSLEWIGY IDPYNADTTY NREFKGKATL TVDKSSSTAF MHLNSLTSE DSAVYYCARK RNNFYFDYWG QGTPLTVSSA KTTPPSVYPL APGCGDTTGS SVTLGCLVKG YFPESVTVTW N SGSLSSSV HTFPALLQSG LYTMSSSVTV PSSTWPSQTV TCSVAHPASS TTVDKKSAAL EVLFQ

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Macromolecule #3: 8E3 Fab light chain

MacromoleculeName: 8E3 Fab light chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.62408 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: YIVMTQSPKS MSMSLGERVT LSCRASEYVG SYVSWYQQKP EQSPKLLIYG ASNRYTGVPD RFAGSGSATD FTLTITSVQA EDLADYHCG QTYNYPTFGG GTKLEIKRAD AAPTVSIFPP SSEQLTSGGA SVVCFLNNFY PKDINVKWKI DGSERQNGVL N SWTDQDSK ...String:
YIVMTQSPKS MSMSLGERVT LSCRASEYVG SYVSWYQQKP EQSPKLLIYG ASNRYTGVPD RFAGSGSATD FTLTITSVQA EDLADYHCG QTYNYPTFGG GTKLEIKRAD AAPTVSIFPP SSEQLTSGGA SVVCFLNNFY PKDINVKWKI DGSERQNGVL N SWTDQDSK DSTYSMSSTL TLTKDEYERH NSYTCEATHK TSTSPIVKSF NRNEC

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Macromolecule #4: Gamma-aminobutyric acid receptor subunit alpha-1

MacromoleculeName: Gamma-aminobutyric acid receptor subunit alpha-1 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 51.818516 KDa
SequenceString: MKKSRGLSDY LWAWTLILST LSGRSYGQPS QDELKDNTTV FTRILDRLLD GYDNRLRPGL GERVTEVKTD IFVTSFGPVS DHDMEYTID VFFRQSWKDE RLKFKGPMTV LRLNNLMASK IWTPDTFFHN GKKSVAHNMT MPNKLLRITE DGTLLYTMRL T VRAECPMH ...String:
MKKSRGLSDY LWAWTLILST LSGRSYGQPS QDELKDNTTV FTRILDRLLD GYDNRLRPGL GERVTEVKTD IFVTSFGPVS DHDMEYTID VFFRQSWKDE RLKFKGPMTV LRLNNLMASK IWTPDTFFHN GKKSVAHNMT MPNKLLRITE DGTLLYTMRL T VRAECPMH LEDFPMDAHA CPLKFGSYAY TRAEVVYEWT REPARSVVVA EDGSRLNQYD LLGQTVDSGI VQSSTGEYVV MT THFHLKR KIGYFVIQTY LPCIMTVILS QVSFWLNRES VPARTVFGVT TVLTMTTLSI SARNSLPKVA YATAMDWFIA VCY AFVFSA LIEFATVNYF TKRGYAWDGK SVVPEKPKKV KDPLIKKNNT YAPTATSYTP NLARGDPGLA TIAKSATIEP KEVK PETKP PEPKKTFNSV SKIDRLSRIA FPLLFGIFNL VYWATYLNRE PQLKAPTPHQ

UniProtKB: Gamma-aminobutyric acid receptor subunit alpha-1

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Macromolecule #5: Gamma-aminobutyric acid receptor subunit beta-2

MacromoleculeName: Gamma-aminobutyric acid receptor subunit beta-2 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 54.697297 KDa
SequenceString: MWRVRKRGYF GIWSFPLIIA AVCAQSVNDP SNMSLVKETV DRLLKGYDIR LRPDFGGPPV AVGMNIDIAS IDMVSEVNMD YTLTMYFQQ AWRDKRLSYN VIPLNLTLDN RVADQLWVPD TYFLNDKKSF VHGVTVKNRM IRLHPDGTVL YGLRITTTAA C MMDLRRYP ...String:
MWRVRKRGYF GIWSFPLIIA AVCAQSVNDP SNMSLVKETV DRLLKGYDIR LRPDFGGPPV AVGMNIDIAS IDMVSEVNMD YTLTMYFQQ AWRDKRLSYN VIPLNLTLDN RVADQLWVPD TYFLNDKKSF VHGVTVKNRM IRLHPDGTVL YGLRITTTAA C MMDLRRYP LDEQNCTLEI ESYGYTTDDI EFYWRGDDNA VTGVTKIELP QFSIVDYKLI TKKVVFSTGS YPRLSLSFKL KR NIGYFIL QTYMPSILIT ILSWVSFWIN YDASAARVAL GITTVLTMTT INTHLRETLP KIPYVKAIDM YLMGCFVFVF MAL LEYALV NYIFFGRGPQ RQKKAAEKAA NANNEKMRLD VNKMDPHENI LLSTLEIKNE MATSEAVMGL GDPRSTMLAY DASS IQYRK AGLPRHSFGR NALERHVAQK KSRLRRRASQ LKITIPDLTD VNAIDRWSRI FFPVVFSFFN IVYWLYYVN

UniProtKB: Gamma-aminobutyric acid receptor subunit beta-2

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Macromolecule #10: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 10 / Number of copies: 1 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #11: GAMMA-AMINO-BUTANOIC ACID

MacromoleculeName: GAMMA-AMINO-BUTANOIC ACID / type: ligand / ID: 11 / Number of copies: 2 / Formula: ABU
Molecular weightTheoretical: 103.12 Da
Chemical component information

ChemComp-ABU:
GAMMA-AMINO-BUTANOIC ACID / neurotransmitter, inhibitor*YM

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Macromolecule #12: 7-methoxy-2-(4-methoxyphenyl)-1,2-dihydro-3H-pyrazolo[4,3-c]quino...

MacromoleculeName: 7-methoxy-2-(4-methoxyphenyl)-1,2-dihydro-3H-pyrazolo[4,3-c]quinolin-3-one
type: ligand / ID: 12 / Number of copies: 1 / Formula: A1CEP
Molecular weightTheoretical: 321.33 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.05 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.74 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 159009
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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