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- EMDB-56081: GABA-A receptor a3b3g2 + a3NB77 + bicuculline -

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Basic information

Entry
Database: EMDB / ID: EMD-56081
TitleGABA-A receptor a3b3g2 + a3NB77 + bicuculline
Map data
Sample
  • Complex: alpha3-beta3-gamma2 GABA-A receptor in complex with bicuculline and nanobody a3NB77
    • Complex: GABA-A receptor
      • Protein or peptide: Gamma-aminobutyric acid receptor subunit alpha-3
      • Protein or peptide: GABA-A receptor beta-3-bril
      • Protein or peptide: Gamma-aminobutyric acid receptor subunit gamma-2
    • Complex: Nanobody a3NB77
      • Protein or peptide: a3NB77
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: bicuculline methochloride
KeywordspLGIC / GABA / Neurotransmission / MEMBRANE PROTEIN
Function / homology
Function and homology information


benzodiazepine receptor activity / extrasynaptic signaling via GABA / cellular response to histamine / GABA receptor activation / negative regulation of synaptic transmission, GABAergic / GABA-gated chloride ion channel activity / GABA-A receptor complex / inhibitory synapse assembly / GABA-A receptor activity / synaptic transmission, GABAergic ...benzodiazepine receptor activity / extrasynaptic signaling via GABA / cellular response to histamine / GABA receptor activation / negative regulation of synaptic transmission, GABAergic / GABA-gated chloride ion channel activity / GABA-A receptor complex / inhibitory synapse assembly / GABA-A receptor activity / synaptic transmission, GABAergic / gamma-aminobutyric acid signaling pathway / postsynaptic specialization membrane / chloride channel activity / Signaling by ERBB4 / chloride channel complex / cytoplasmic vesicle membrane / dendrite membrane / chloride transmembrane transport / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / GABA-ergic synapse / dendritic spine / postsynaptic membrane / postsynapse / axon / plasma membrane
Similarity search - Function
Gamma-aminobutyric-acid A receptor, alpha 3 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/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 ...Gamma-aminobutyric-acid A receptor, alpha 3 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/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-3
Similarity search - Component
Biological speciesHomo sapiens (human) / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.87 Å
AuthorsShang C / Nestorow SA / Miller PS
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
DepositionDec 15, 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_56081.png

Downloads & links

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Map

FileDownload / File: emd_56081.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 384 pix.
= 249.984 Å		0.65 Å/pix.
x 384 pix.
= 249.984 Å		0.65 Å/pix.
x 384 pix.
= 249.984 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.651 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0495
Minimum - Maximum-0.11692786 - 0.23900008
Average (Standard dev.)0.0003807125 (±0.009016209)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 249.98401 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_56081_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_56081_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : alpha3-beta3-gamma2 GABA-A receptor in complex with bicuculline a...

EntireName: alpha3-beta3-gamma2 GABA-A receptor in complex with bicuculline and nanobody a3NB77
Components
  • Complex: alpha3-beta3-gamma2 GABA-A receptor in complex with bicuculline and nanobody a3NB77
    • Complex: GABA-A receptor
      • Protein or peptide: Gamma-aminobutyric acid receptor subunit alpha-3
      • Protein or peptide: GABA-A receptor beta-3-bril
      • Protein or peptide: Gamma-aminobutyric acid receptor subunit gamma-2
    • Complex: Nanobody a3NB77
      • Protein or peptide: a3NB77
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: bicuculline methochloride

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Supramolecule #1: alpha3-beta3-gamma2 GABA-A receptor in complex with bicuculline a...

SupramoleculeName: alpha3-beta3-gamma2 GABA-A receptor in complex with bicuculline and nanobody a3NB77
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Details: The heteropentameric alpha3beta3gamma2 GABA(A) receptor was recombinantly expressed in HEK293 cells. Constructs were engineered with the M3- M4 intracellular domain replaced either by a GLVI ...Details: The heteropentameric alpha3beta3gamma2 GABA(A) receptor was recombinantly expressed in HEK293 cells. Constructs were engineered with the M3- M4 intracellular domain replaced either by a GLVI linker sequence (SQPARAA) or by a modified GLVI sequence containing Escherichia coli cytochrome B562RIL41. The sample was prepared in the presence of bicuculline and nanobody a3NB77
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: GABA-A receptor

SupramoleculeName: GABA-A receptor / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Nanobody a3NB77

SupramoleculeName: Nanobody a3NB77 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: Lama glama (llama)

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Macromolecule #1: Gamma-aminobutyric acid receptor subunit alpha-3

MacromoleculeName: Gamma-aminobutyric acid receptor subunit alpha-3 / type: protein_or_peptide / ID: 1
Details: Glvi linker sequence (SQPARAA). Region substituted: Arg337-Ser425,Glvi linker sequence (SQPARAA). Region substituted: Arg337-Ser425
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 43.43982 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QGESRRQEPG DFVKQDIGGL SPKHAPDIPD DSTDNITIFT RILDRLLDGY DNRLRPGLGD AVTEVKTDIY VTSFGPVSDT DMEYTIDVF FRQTWHDERL KFDGPMKILP LNNLLASKIW TPDTFFHNGK KSVAHNMTTP NKLLRLVDNG TLLYTMRLTI H AECPMHLE ...String:
QGESRRQEPG DFVKQDIGGL SPKHAPDIPD DSTDNITIFT RILDRLLDGY DNRLRPGLGD AVTEVKTDIY VTSFGPVSDT DMEYTIDVF FRQTWHDERL KFDGPMKILP LNNLLASKIW TPDTFFHNGK KSVAHNMTTP NKLLRLVDNG TLLYTMRLTI H AECPMHLE DFPMDVHACP LKFGSYAYTT AEVVYSWTLG KNKSVEVAQD GSRLNQYDLL GHVVGTEIIR SSTGEYVVMT TH FHLKRKI GYFVIQTYLP CIMTVILSQV SFWLNRESVP ARTVFGVTTV LTMTTLSISA RNSLPKVAYA TAMDWFIAVC YAF VFSALI EFATVNYFTK SQPARAAKVD KISRIIFPVL FAIFNLVYWA TYVNRESAIK GMIRKQG

UniProtKB: Gamma-aminobutyric acid receptor subunit alpha-3, Gamma-aminobutyric acid receptor subunit alpha-3

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Macromolecule #2: GABA-A receptor beta-3-bril

MacromoleculeName: GABA-A receptor beta-3-bril / type: protein_or_peptide / ID: 2
Details: Modified glvi sequence containing the Escherichia coli soluble cytochrome B562RIL41 (BRIL, amino acids 23-130, ADLE...QKYL, Uniprot P0ABE7) to give the sequence SQPAGT-BRIL-TGRAA. Linker ...Details: Modified glvi sequence containing the Escherichia coli soluble cytochrome B562RIL41 (BRIL, amino acids 23-130, ADLE...QKYL, Uniprot P0ABE7) to give the sequence SQPAGT-BRIL-TGRAA. Linker regions substituted Gly308-Asn421. This BRIL domain was present in the protein but not resolved in the cryo-EM density and is therefore not included in the atomic model.
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

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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
Details: Includes an 1D4 tag at C-terminus of the sequence (TETSQVAPA), this is not resolved in density and not modelled. Glvi linker sequence (SQPARAA), region substituted Ser322-Ala408,Includes an ...Details: Includes an 1D4 tag at C-terminus of the sequence (TETSQVAPA), this is not resolved in density and not modelled. Glvi linker sequence (SQPARAA), region substituted Ser322-Ala408,Includes an 1D4 tag at C-terminus of the sequence (TETSQVAPA), this is not resolved in density and not modelled. Glvi linker sequence (SQPARAA), region substituted Ser322-Ala408
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: a3NB77

MacromoleculeName: a3NB77 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 13.594054 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLVESGGG LVQAGGSLRL TCVASGTIFS SSTMGWYRQA PGKQRELVAY ITTSGDTLYT PSVKGRFTIS RENAKNTVYL QMSSLKPED TAVYYCYSYF GSGRWGEGTQ VTVSSHHHHH HEPEA

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Macromolecule #9: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 9 / Number of copies: 5 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #10: bicuculline methochloride

MacromoleculeName: bicuculline methochloride / type: ligand / ID: 10 / Number of copies: 2 / Formula: H0Z
Molecular weightTheoretical: 367.352 Da
Chemical component information

ChemComp-H0Z:
bicuculline methochloride

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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: 7.6
Details: 75 millimolar sodium chloride; 12.5 millimolar HEPES, pH 7.6; 1.5 millimolar 1D4 peptide
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsNanodisc-reconstituted alpha3beta3gamma2 GABA-A receptor in complex with with bicuculline and nanobody a3NB77

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Electron microscopy

MicroscopeTFS KRIOS
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / #0 - Number real images: 4031 / #0 - Average electron dose: 51.25 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / #1 - Average electron dose: 51.25 e/Å2 / #2 - Image recording ID: 3 / #2 - Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / #2 - Average electron dose: 51.25 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing #1

Image processing ID1
Image recording ID1
Particle selection#0 - Number selected: 630021 / #1 - Number selected: 630021 / #2 - Number selected: 630021
CTF correctionSoftware - Name: cryoSPARC (ver. 4.4.1 to 4.7.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup model#0 - Type of model: NONE
#0 - Details: An ab initio 3D reconstruction was generated from experimental 2D class averages in cryoSPARC without the use of any external reference, and was used as the startup model for future refinements.
#1 - Type of model: NONE
#1 - Details: An ab initio 3D reconstruction was generated from experimental 2D class averages in cryoSPARC without the use of any external reference, and was used as the startup model for future refinements.
#2 - Type of model: NONE
#2 - Details: An ab initio 3D reconstruction was generated from experimental 2D class averages in cryoSPARC without the use of any external reference, and was used as the startup model for future refinements.
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1 to 4.7.1) / Number images used: 152562
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 4.4.1 to 4.7.1)
Details: Particle orientations were assigned by projection matching during iterative refinement in cryoSPARC
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 4.4.1 to 4.7.1)
Details: Final orientations determined by projection matching during non-uniform refinement in cryoSPARC.
FSC plot (resolution estimation)

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Image processing #2

Image processing ID2
Image recording ID2
Particle selectionNumber selected: 630021
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup model#0 - Type of model: NONE / #1 - Type of model: NONE / #2 - Type of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1 to 4.7.1) / Number images used: 152562
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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Image processing #3

Image processing ID3
Image recording ID3
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup model#0 - Type of model: NONE / #1 - Type of model: NONE / #2 - Type of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 152562
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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Image processing #4

Image processing ID4
Image recording ID1
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup model#0 - Type of model: NONE / #1 - Type of model: NONE / #2 - Type of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 152562
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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