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- EMDB-53213: GABA-A receptor a2b3g2 + a2NB00(PAM) + GABA -

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Basic information

Entry
Database: EMDB / ID: EMD-53213
TitleGABA-A receptor a2b3g2 + a2NB00(PAM) + GABA
Map dataGABA-A receptor a2b3g2 a2VHH00
Sample
  • Complex: GABA-A receptor a2b3g2 + a2VHH00(PAM) + GABA
    • Protein or peptide: Gamma-aminobutyric acid receptor subunit alpha-2
    • Protein or peptide: Gamma-aminobutyric acid receptor subunit beta-3,Soluble cytochrome b562
    • Protein or peptide: Gamma-aminobutyric acid receptor subunit gamma-2
    • Protein or peptide: a2NB00
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: GAMMA-AMINO-BUTANOIC ACID
KeywordspLGIC GABA Neurotransmission / MEMBRANE PROTEIN
Function / homology
Function and homology information


benzodiazepine receptor activity / inhibitory synapse / extrasynaptic signaling via GABA / cellular response to histamine / inner ear receptor cell development / GABA receptor activation / negative regulation of synaptic transmission, GABAergic / innervation / GABA-gated chloride ion channel activity / GABA-A receptor complex ...benzodiazepine receptor activity / inhibitory synapse / extrasynaptic signaling via GABA / cellular response to histamine / inner ear receptor cell development / GABA receptor activation / negative regulation of synaptic transmission, GABAergic / innervation / GABA-gated chloride ion channel activity / GABA-A receptor complex / inhibitory synapse assembly / GABA-A receptor activity / roof of mouth development / inhibitory postsynaptic potential / synaptic transmission, GABAergic / gamma-aminobutyric acid signaling pathway / postsynaptic specialization membrane / chloride channel activity / Signaling by ERBB4 / cochlea development / chloride channel complex / cytoplasmic vesicle membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dendrite membrane / chloride transmembrane transport / electron transport chain / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / GABA-ergic synapse / synaptic vesicle membrane / dendritic spine / electron transfer activity / periplasmic space / postsynaptic membrane / postsynapse / iron ion binding / axon / neuronal cell body / heme binding / cell surface / signal transduction / identical protein binding / plasma membrane
Similarity search - Function
Gamma-aminobutyric-acid A receptor, alpha 2 subunit / : / Gamma-aminobutyric-acid A receptor, gamma 2 subunit / Gamma-aminobutyric acid receptor subunit gamma-1/4 / 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, alpha 2 subunit / : / Gamma-aminobutyric-acid A receptor, gamma 2 subunit / Gamma-aminobutyric acid receptor subunit gamma-1/4 / 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 / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / 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
Soluble cytochrome b562 / Gamma-aminobutyric acid receptor subunit gamma-2 / Gamma-aminobutyric acid receptor subunit beta-3 / Gamma-aminobutyric acid receptor subunit alpha-2
Similarity search - Component
Biological speciesHomo sapiens (human) / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsMiller PS / Gonzalez-Prada JE
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M024709/1 United Kingdom
CitationJournal: Sci Adv / Year: 2026
Title: Determining the molecular and physiological actions of subtype-selective nanobodies of GABA receptors.
Authors: Jose Enrique Gonzalez-Prada / Sulin Liu / Chuhan Shang / Chloe S Chernoff / Damian P Bright / Martin Mortensen / Charlotte F Jones / Stephanie Nestorow / Vikram Babu Kasaragod / Wan-Na Chen ...Authors: Jose Enrique Gonzalez-Prada / Sulin Liu / Chuhan Shang / Chloe S Chernoff / Damian P Bright / Martin Mortensen / Charlotte F Jones / Stephanie Nestorow / Vikram Babu Kasaragod / Wan-Na Chen / Saad Hannan / Jianchong Zhou / Alexander W E Dunn / Asma Soltani / Richard J Turner / Natasha M Duggan / Yin Yuan / Ayla A Wahid / Steven W Hardwick / Suzanne Scott / Dimitri Y Chirgadze / Els Pardon / Jan Steyaert / A Radu Aricescu / Ole Paulsen / David Belin / Trevor G Smart / Paul S Miller /
Abstract: γ-Aminobutyric acid type-A (GABA) receptors are the principal mediators of inhibitory neurotransmission in the human central nervous system. The α- and α-containing subtypes have tightly ...γ-Aminobutyric acid type-A (GABA) receptors are the principal mediators of inhibitory neurotransmission in the human central nervous system. The α- and α-containing subtypes have tightly controlled spatial expression profiles, which influence anxiety, nociception, epilepsy, and autism. α/α-Selective small molecules compromise on strength of effect (efficacy) to avoid off-subtype modulation. To break this pharmacological deadlock, we study here a panel of nanobodies (NBs) raised against α- and α-containing GABA receptors. We identify subtype selective silent binders, positive allosteric modulators (PAMs), and inhibitors. Cryo-electron microscopy structures explain the binding modes and molecular mechanisms of action of representative NBs. Modulators exhibit distinct synaptic and extrasynaptic functional profiles in brain slices and neuronal networks and can reduce anxiety in vivo. These selective and efficacious NBs (whether inhibitors or positive modulators) enable strong yet precise pharmacological control of α/α-containing subtypes to advance basic research and as potential therapeutic leads to treat neuropsychiatric disorders.
History
DepositionMar 19, 2025-
Header (metadata) releaseAug 26, 2026-
Map releaseAug 26, 2026-
UpdateAug 26, 2026-
Current statusAug 26, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53213.png

Downloads & links

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Map

FileDownload / File: emd_53213.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGABA-A receptor a2b3g2 a2VHH00
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 384 pix.
= 249.6 Å		0.65 Å/pix.
x 384 pix.
= 249.6 Å		0.65 Å/pix.
x 384 pix.
= 249.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.65 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0416
Minimum - Maximum-0.11664299 - 0.25799885
Average (Standard dev.)0.00024451345 (±0.007999965)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 249.59999 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: GABA-A receptor a2b3g2 a2VHH00

Fileemd_53213_half_map_1.map
AnnotationGABA-A receptor a2b3g2 a2VHH00
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: GABA-A receptor a2b3g2 a2VHH00

Fileemd_53213_half_map_2.map
AnnotationGABA-A receptor a2b3g2 a2VHH00
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : GABA-A receptor a2b3g2 + a2VHH00(PAM) + GABA

EntireName: GABA-A receptor a2b3g2 + a2VHH00(PAM) + GABA
Components
  • Complex: GABA-A receptor a2b3g2 + a2VHH00(PAM) + GABA
    • Protein or peptide: Gamma-aminobutyric acid receptor subunit alpha-2
    • Protein or peptide: Gamma-aminobutyric acid receptor subunit beta-3,Soluble cytochrome b562
    • Protein or peptide: Gamma-aminobutyric acid receptor subunit gamma-2
    • Protein or peptide: a2NB00
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: GAMMA-AMINO-BUTANOIC ACID

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Supramolecule #1: GABA-A receptor a2b3g2 + a2VHH00(PAM) + GABA

SupramoleculeName: GABA-A receptor a2b3g2 + a2VHH00(PAM) + GABA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 240 KDa

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

MacromoleculeName: Gamma-aminobutyric acid receptor subunit alpha-2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.452406 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: NIQEDEAKNN ITIFTRILDR LLDGYDNRLR PGLGDSITEV FTNIYVTSFG PVSDTDMEYT IDVFFRQKWK DERLKFKGPM NILRLNNLM ASKIWTPDTF FHNGKKSVAH NMTMPNKLLR IQDDGTLLYT MRLTVQAECP MHLEDFPMDA HSCPLKFGSY A YTTSEVTY ...String:
NIQEDEAKNN ITIFTRILDR LLDGYDNRLR PGLGDSITEV FTNIYVTSFG PVSDTDMEYT IDVFFRQKWK DERLKFKGPM NILRLNNLM ASKIWTPDTF FHNGKKSVAH NMTMPNKLLR IQDDGTLLYT MRLTVQAECP MHLEDFPMDA HSCPLKFGSY A YTTSEVTY IWTYNASDSV QVAPDGSRLN QYDLLGQSIG KETIKSSTGE YTVMTAHFHL KRKIGYFVIQ TYLPCIMTVI LS QVSFWLN RESVPARTVF GVTTVLTMTT LSISARNSLP KVAYATAMDW FIAVCYAFVF SALIEFATVN YFTKSQPARA AKI DRMSRI VFPVLFGTFN LVYWATYLNR EPVLGVSP

UniProtKB: Gamma-aminobutyric acid receptor subunit alpha-2, Gamma-aminobutyric acid receptor subunit alpha-2

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Macromolecule #2: Gamma-aminobutyric acid receptor subunit beta-3,Soluble cytochrom...

MacromoleculeName: Gamma-aminobutyric acid receptor subunit beta-3,Soluble cytochrome b562
type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 51.615117 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QSVNDPGNMS FVKETVDKLL KGYDIRLRPD FGGPPVCVGM NIDIASIDMV SEVNMDYTLT MYFQQYWRDK RLAYSGIPLN LTLDNRVAD QLWVPDTYFL NDKKSFVHGV TVKNRMIRLH PDGTVLYGLR ITTTAACMMD LRRYPLDEQN CTLEIESYGY T TDDIEFYW ...String:
QSVNDPGNMS FVKETVDKLL KGYDIRLRPD FGGPPVCVGM NIDIASIDMV SEVNMDYTLT MYFQQYWRDK RLAYSGIPLN LTLDNRVAD QLWVPDTYFL NDKKSFVHGV TVKNRMIRLH PDGTVLYGLR ITTTAACMMD LRRYPLDEQN CTLEIESYGY T TDDIEFYW RGGDKAVTGV ERIELPQFSI VEHRLVSRNV VFATGAYPRL SLSFRLKRNI GYFILQTYMP SILITILSWV SF WINYDAS AARVALGITT VLTMTTINTH LRETLPKIPY VKAIDMYLMG CFVFVFLALL EYAFVNYIFF SQPAGTADLE DNW ETLNDN LKVIEKADNA AQVKDALTKM RAAALDAQKA TPPKLEDKSP DSPEMKDFRH GFDILVGQID DALKLANEGK VKEA QAAAE QLKTTRNAYI QKYLTGRAAA IDRWSRIVFP FTFSLFNLVY WLYYVN

UniProtKB: Gamma-aminobutyric acid receptor subunit beta-3, Soluble cytochrome b562, Gamma-aminobutyric acid receptor subunit beta-3

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Macromolecule #3: Gamma-aminobutyric acid receptor subunit gamma-2

MacromoleculeName: Gamma-aminobutyric acid receptor subunit gamma-2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 42.798875 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QKSDDDYEDY TSNKTWVLTP KVPEGDVTVI LNNLLEGYDN KLRPDIGVKP TLIHTDMYVN SIGPVNAINM EYTIDIFFAQ TWYDRRLKF NSTIKVLRLN SNMVGKIWIP DTFFRNSKKA DAHWITTPNR MLRIWNDGRV LYTLRLTIDA ECQLQLHNFP M DEHSCPLE ...String:
QKSDDDYEDY TSNKTWVLTP KVPEGDVTVI LNNLLEGYDN KLRPDIGVKP TLIHTDMYVN SIGPVNAINM EYTIDIFFAQ TWYDRRLKF NSTIKVLRLN SNMVGKIWIP DTFFRNSKKA DAHWITTPNR MLRIWNDGRV LYTLRLTIDA ECQLQLHNFP M DEHSCPLE FSSYGYPREE IVYQWKRSSV EVGDTRSWRL YQFSFVGLRN TTEVVKTTSG DYVVMSVYFD LSRRMGYFTI QT YIPCTLI VVLSWVSFWI NKDAVPARTS LGITTVLTMT TLSTIARKSL PKVSYVTAMD LFVSVCFIFV FSALVEYGTL HYF VSSQPA RAAKMDSYAR IFFPTAFCLF NLVYWVSYLY LGTGTGTETS QVAPA

UniProtKB: Gamma-aminobutyric acid receptor subunit gamma-2, Gamma-aminobutyric acid receptor subunit gamma-2

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Macromolecule #4: a2NB00

MacromoleculeName: a2NB00 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 14.391739 KDa
Recombinant expressionOrganism: Lama glama (llama)
SequenceString:
QVQLVESGGA LVQAGGSLRL SCAASGFTFD DYAIGWFRRA PGKEREGVSC ISSGGGSTYY ADSVKGRFTI SSDNAKNTVY LQMNSLKPE DTAVYFCAAV GYSSSCNPLW YDYWGQGTQV TVSSHHHHHH EPEA

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Macromolecule #11: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 11 / Number of copies: 3 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #12: GAMMA-AMINO-BUTANOIC ACID

MacromoleculeName: GAMMA-AMINO-BUTANOIC ACID / type: ligand / ID: 12 / 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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 51.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: DIFFRACTION / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.9 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: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 297968
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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