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- PDB-9tns: GABA-A receptor a3b3g2 + GABA-PRE + a3NB83 -

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Basic information

Entry
Database: PDB / ID: 9tns
TitleGABA-A receptor a3b3g2 + GABA-PRE + a3NB83
Components
  • (Gamma-aminobutyric acid receptor subunit ...) x 2
  • GABA-A receptor beta-3-bril
  • a3NB83
KeywordsMEMBRANE PROTEIN / pLGIC / GABA / Neurotransmission
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-AMINO-BUTANOIC ACID / Gamma-aminobutyric acid receptor subunit gamma-2 / Gamma-aminobutyric acid receptor subunit alpha-3
Similarity search - Component
Biological speciesHomo sapiens (human)
Lama glama (llama)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsShang, C. / Nestorow, S.A. / Miller, P.S.
Funding support United Kingdom, 1items
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 16, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gamma-aminobutyric acid receptor subunit alpha-3
B: GABA-A receptor beta-3-bril
C: Gamma-aminobutyric acid receptor subunit gamma-2
D: Gamma-aminobutyric acid receptor subunit alpha-3
E: GABA-A receptor beta-3-bril
F: a3NB83
hetero molecules


Theoretical massNumber of molelcules
Total (without water)253,83019
Polymers247,3776
Non-polymers6,45313
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Gamma-aminobutyric acid receptor subunit ... , 2 types, 3 molecules ADC

#1: Protein Gamma-aminobutyric acid receptor subunit alpha-3 / GABA(A) receptor subunit alpha-3 / GABAAR subunit alpha-3


Mass: 43382.766 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Glvi linker sequence (SQPARAA). Region substituted: Arg337-Ser425,Glvi linker sequence (SQPARAA). Region substituted: Arg337-Ser425
Source: (gene. exp.) Homo sapiens (human) / Gene: GABRA3 / Production host: Homo sapiens (human) / References: UniProt: P34903
#3: Protein Gamma-aminobutyric acid receptor subunit gamma-2 / GABA(A) receptor subunit gamma-2 / GABAAR subunit gamma-2


Mass: 42798.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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
Source: (gene. exp.) Homo sapiens (human) / Gene: GABRG2 / Production host: Homo sapiens (human) / References: UniProt: P18507

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Protein / Antibody / Non-polymers , 3 types, 5 molecules BEF

#10: Chemical ChemComp-ABU / GAMMA-AMINO-BUTANOIC ACID / GAMMA(AMINO)-BUTYRIC ACID


Mass: 103.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H9NO2 / Feature type: SUBJECT OF INVESTIGATION / Comment: neurotransmitter, inhibitor*YM
#2: Protein GABA-A receptor beta-3-bril


Mass: 51615.117 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
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.
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Antibody a3NB83


Mass: 14582.058 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Homo sapiens (human)

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Sugars , 5 types, 11 molecules

#5: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1235.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1_e6-g1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#6: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#7: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#8: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...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-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#9: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeDetails (eV)Entity IDParent-IDSource
1alpha3-beta3-gamma2 GABA-A receptor in complex with GABA and nanobody a3NB83COMPLEXThe 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 GABA and nanobody a3NB83#1-#40RECOMBINANT
2GABA-A receptorCOMPLEX#1-#31RECOMBINANT
3Nanobody a3NB83COMPLEX#41RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
32Homo sapiens (human)9606
33Lama glama (llama)9844
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDCellPlasmid
21Homo sapiens (human)9606
22Homo sapiens (human)9606Expi293F GnTI-pHLsec
33Homo sapiens (human)9606Expi293FpHLsec
Buffer solutionpH: 7.6
Details: 75 millimolar sodium chloride; 12.5 millimolar HEPES, pH 7.6; 1.5 millimolar 1D4 peptide
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Nanodisc-reconstituted alpha3beta3gamma2 GABA-A receptor in complex with with GABA and nanobody a3NB83
Specimen supportGrid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recording
IDImaging-IDAverage exposure time (sec.)Electron dose (e/Å2)Film or detector modelNum. of real images
114.3950.47FEI FALCON IV (4k x 4k)1838
214.3950.47FEI FALCON IV (4k x 4k)1838
314.3950.47FEI FALCON IV (4k x 4k)1838

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Processing

EM software
IDNameVersionCategoryImage processing-ID
1ARP/wARP1.0.9particle selection1
4ARP/wARP1.0.9CTF correction1
7UCSF Chimera1.8model fitting
9PHENIX1.20.1_4487model refinement
10cryoSPARC4.4.1 to 4.7.1initial Euler assignment1
11cryoSPARC4.4.1 to 4.7.1final Euler assignment1
13cryoSPARC4.4.1 to 4.7.13D reconstruction1
14ARP/wARP1.0.9particle selection2
15ARP/wARP1.0.9CTF correction2
19cryoSPARC4.4.1 to 4.7.13D reconstruction2
20cryoSPARC4.4.1 to 4.7.1particle selection3
21cryoSPARCparticle selection3
26cryoSPARC3D reconstruction3
27cryoSPARCparticle selection4
32cryoSPARC3D reconstruction4
33ARP/wARP1.0.9particle selection5
34ARP/wARP1.0.9CTF correction5
35cryoSPARC4.4.1 to 4.7.1initial Euler assignment5
36cryoSPARC4.4.1 to 4.7.1final Euler assignment5
38cryoSPARC4.4.1 to 4.7.13D reconstruction5
Image processing
IDImage recording-ID
11
22
33
41
51
CTF correction
IDEM image processing-IDType
11PHASE FLIPPING AND AMPLITUDE CORRECTION
22PHASE FLIPPING AND AMPLITUDE CORRECTION
33PHASE FLIPPING AND AMPLITUDE CORRECTION
44PHASE FLIPPING AND AMPLITUDE CORRECTION
55PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selection
IDImage processing-IDNum. of particles selected
11314781
21314781
31314781
42314781
52314781
62314781
73
83
93
104
114
124
135314781
145314781
155314781
Symmetry
IDImage processing-IDEntry-IDPoint symmetry
119TNSC1 (asymmetric)
219TNSC1 (asymmetric)
319TNSC1 (asymmetric)
419TNSC1 (asymmetric)
519TNSC1 (asymmetric)
659TNSC1 (asymmetric)
759TNSC1 (asymmetric)
859TNSC1 (asymmetric)
959TNSC1 (asymmetric)
1059TNSC1 (asymmetric)
3D reconstruction
IDResolution (Å)Resolution methodNum. of particlesImage processing-IDEntry-IDSymmetry type
12.8FSC 0.143 CUT-OFF8190019TNSPOINT
22.8FSC 0.143 CUT-OFF8190019TNSPOINT
32.8FSC 0.143 CUT-OFF8190019TNSPOINT
42.8FSC 0.143 CUT-OFF8190019TNSPOINT
52.8FSC 0.143 CUT-OFF8190019TNSPOINT
62.8FSC 0.143 CUT-OFF8190029TNSPOINT
72.8FSC 0.143 CUT-OFF8190029TNSPOINT
82.8FSC 0.143 CUT-OFF8190029TNSPOINT
92.8FSC 0.143 CUT-OFF8190029TNSPOINT
102.8FSC 0.143 CUT-OFF8190029TNSPOINT
112.8FSC 0.143 CUT-OFF8190039TNSPOINT
122.8FSC 0.143 CUT-OFF8190039TNSPOINT
132.8FSC 0.143 CUT-OFF8190039TNSPOINT
142.8FSC 0.143 CUT-OFF8190039TNSPOINT
152.8FSC 0.143 CUT-OFF8190039TNSPOINT
162.8FSC 0.143 CUT-OFF8190049TNSPOINT
172.8FSC 0.143 CUT-OFF8190049TNSPOINT
182.8FSC 0.143 CUT-OFF8190049TNSPOINT
192.8FSC 0.143 CUT-OFF8190049TNSPOINT
202.8FSC 0.143 CUT-OFF8190049TNSPOINT
212.8FSC 0.143 CUT-OFF8190059TNSPOINT
222.8FSC 0.143 CUT-OFF8190059TNSPOINT
232.8FSC 0.143 CUT-OFF8190059TNSPOINT
242.8FSC 0.143 CUT-OFF8190059TNSPOINT
252.8FSC 0.143 CUT-OFF8190059TNSPOINT
RefinementHighest resolution: 2.8 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00315320
ELECTRON MICROSCOPYf_angle_d0.55720844
ELECTRON MICROSCOPYf_dihedral_angle_d5.1262251
ELECTRON MICROSCOPYf_chiral_restr0.0822468
ELECTRON MICROSCOPYf_plane_restr0.0042532

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