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- PDB-9slm: GABA-A a4b3d receptor in complex with GABA and Nb24 -

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Basic information

Entry
Database: PDB / ID: 9slm
TitleGABA-A a4b3d receptor in complex with GABA and Nb24
Components
  • (Gamma-aminobutyric acid receptor subunit ...) x 3
  • Nanobody Nb24
KeywordsMEMBRANE PROTEIN / pLGIC / GABA / Neurotransmission / Extrasynaptic
Function / homology
Function and homology information


GABA receptor activation / 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 receptor activation / 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 / extracellular ligand-gated monoatomic ion channel activity / cytoplasmic vesicle membrane / dendrite membrane / chloride transmembrane transport / central nervous system development / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / GABA-ergic synapse / dendritic spine / postsynaptic membrane / postsynapse / axon / neuronal cell body / dendrite / glutamatergic synapse / cell surface / signal transduction / identical protein binding / plasma membrane
Similarity search - Function
Gamma-aminobutyric-acid A receptor, alpha 4 subunit / Gamma-aminobutyric-acid A receptor delta 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 ...Gamma-aminobutyric-acid A receptor, alpha 4 subunit / Gamma-aminobutyric-acid A receptor delta 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-AMINO-BUTANOIC ACID / DECANE / 1,2-DIPALMITOYL-SN-GLYCERO-3-PHOSPHATE / Gamma-aminobutyric acid type A receptor subunit alpha4 / Gamma-aminobutyric acid receptor subunit delta / Gamma-aminobutyric acid receptor subunit beta-3 / Gamma-aminobutyric acid receptor subunit alpha-4
Similarity search - Component
Biological speciesHomo sapiens (human)
Lama glama (llama)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.27 Å
AuthorsNestorow, S. / Miller, P.S.
Funding support United Kingdom, Switzerland, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M024709/1 United Kingdom
F. Hoffmann-La Roche LTD Switzerland
CitationJournal: Nat Commun / Year: 2026
Title: Molecular arrangement and modulation of extrasynaptic alpha beta delta GABAA receptors
Authors: Nestorow, S.A. / Chen, W.N. / Bertrand, D. / Wahid, A.A. / Wyatt, C.E. / Mortensen, M. / Clairfeuille, T. / Reutlinger, M. / Friz, G. / Pardon, E. / Steyaert, J. / Ladds, G. / Cecere, G. / ...Authors: Nestorow, S.A. / Chen, W.N. / Bertrand, D. / Wahid, A.A. / Wyatt, C.E. / Mortensen, M. / Clairfeuille, T. / Reutlinger, M. / Friz, G. / Pardon, E. / Steyaert, J. / Ladds, G. / Cecere, G. / Smart, T.G. / Hernandez, M.C. / Joedicke, L. / Miller, P.S.
History
DepositionSep 4, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 2, 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-4,Gamma-aminobutyric acid type A receptor subunit alpha4
B: Gamma-aminobutyric acid receptor subunit beta-3
C: Gamma-aminobutyric acid receptor subunit alpha-4,Gamma-aminobutyric acid type A receptor subunit alpha4
D: Gamma-aminobutyric acid receptor subunit beta-3
E: Gamma-aminobutyric acid receptor subunit delta
F: Nanobody Nb24
G: Nanobody Nb24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)266,06124
Polymers261,8987
Non-polymers4,16317
Water362
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 ... , 3 types, 5 molecules ACBDE

#1: Protein Gamma-aminobutyric acid receptor subunit alpha-4,Gamma-aminobutyric acid type A receptor subunit alpha4 / GABA(A) receptor subunit alpha-4 / GABAAR subunit alpha-4


Mass: 41783.336 Da / Num. of mol.: 2 / Mutation: M120T
Source method: isolated from a genetically manipulated source
Details: Glvi linker sequence (SQPARAA) substituted between Ile311-Ser481. M120T mutation.,Glvi linker sequence (SQPARAA) substituted between Ile311-Ser481. M120T mutation.,Glvi linker sequence ...Details: Glvi linker sequence (SQPARAA) substituted between Ile311-Ser481. M120T mutation.,Glvi linker sequence (SQPARAA) substituted between Ile311-Ser481. M120T mutation.,Glvi linker sequence (SQPARAA) substituted between Ile311-Ser481. M120T mutation.,Glvi linker sequence (SQPARAA) substituted between Ile311-Ser481. M120T mutation.,Glvi linker sequence (SQPARAA) substituted between Ile311-Ser481. M120T mutation.,Glvi linker sequence (SQPARAA) substituted between Ile311-Ser481. M120T mutation.,Glvi linker sequence (SQPARAA) substituted between Ile311-Ser481. M120T mutation.,Glvi linker sequence (SQPARAA) substituted between Ile311-Ser481. M120T mutation.,Glvi linker sequence (SQPARAA) substituted between Ile311-Ser481. M120T mutation.,Glvi linker sequence (SQPARAA) substituted between Ile311-Ser481. M120T mutation.,Glvi linker sequence (SQPARAA) substituted between Ile311-Ser481. M120T mutation.,Glvi linker sequence (SQPARAA) substituted between Ile311-Ser481. M120T mutation.,Glvi linker sequence (SQPARAA) substituted between Ile311-Ser481. M120T mutation.,Glvi linker sequence (SQPARAA) substituted between Ile311-Ser481. M120T mutation.,Glvi linker sequence (SQPARAA) substituted between Ile311-Ser481. M120T mutation.,Glvi linker sequence (SQPARAA) substituted between Ile311-Ser481. M120T mutation.,Glvi linker sequence (SQPARAA) substituted between Ile311-Ser481. M120T mutation.,Glvi linker sequence (SQPARAA) substituted between Ile311-Ser481. M120T mutation.,Glvi linker sequence (SQPARAA) substituted between Ile311-Ser481. M120T mutation.,Glvi linker sequence (SQPARAA) substituted between Ile311-Ser481. M120T mutation.,Glvi linker sequence (SQPARAA) substituted between Ile311-Ser481. M120T mutation.,Glvi linker sequence (SQPARAA) substituted between Ile311-Ser481. M120T mutation.,Glvi linker sequence (SQPARAA) substituted between Ile311-Ser481. M120T mutation.,Glvi linker sequence (SQPARAA) substituted between Ile311-Ser481. M120T mutation.,Glvi linker sequence (SQPARAA) substituted between Ile311-Ser481. M120T mutation.,Glvi linker sequence (SQPARAA) substituted between Ile311-Ser481. M120T mutation.,Glvi linker sequence (SQPARAA) substituted between Ile311-Ser481. M120T mutation.,Glvi linker sequence (SQPARAA) substituted between Ile311-Ser481. M120T mutation.,Glvi linker sequence (SQPARAA) substituted between Ile311-Ser481. M120T mutation.,Glvi linker sequence (SQPARAA) substituted between Ile311-Ser481. M120T mutation.,Glvi linker sequence (SQPARAA) substituted between Ile311-Ser481. M120T mutation.,Glvi linker sequence (SQPARAA) substituted between Ile311-Ser481. M120T mutation.
Source: (gene. exp.) Homo sapiens (human) / Gene: Gabra4, GABRA4 / Production host: Homo sapiens (human) / References: UniProt: Q9D6F4, UniProt: F6UBA8
#2: Protein Gamma-aminobutyric acid receptor subunit beta-3 / GABA(A) receptor subunit beta-3 / GABAAR subunit beta-3


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.,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.,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.,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.,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.,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.,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.,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.,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.,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.,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.,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.,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.,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.,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.,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.,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.,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.,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.,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.,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.,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.,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.,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.,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.,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.,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.,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.,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.,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.,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.,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) / Gene: GABRB3 / Production host: Homo sapiens (human) / References: UniProt: P28472
#3: Protein Gamma-aminobutyric acid receptor subunit delta / GABA(A) receptor subunit delta / GABAAR subunit delta


Mass: 48233.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Includes an SBP tag at start of the sequence, this is not resolved in density and not modelled. Glvi linker sequence (SQPARAA) substituted between Asp312-Asp401.,Includes an SBP tag at start ...Details: Includes an SBP tag at start of the sequence, this is not resolved in density and not modelled. Glvi linker sequence (SQPARAA) substituted between Asp312-Asp401.,Includes an SBP tag at start of the sequence, this is not resolved in density and not modelled. Glvi linker sequence (SQPARAA) substituted between Asp312-Asp401.,Includes an SBP tag at start of the sequence, this is not resolved in density and not modelled. Glvi linker sequence (SQPARAA) substituted between Asp312-Asp401.,Includes an SBP tag at start of the sequence, this is not resolved in density and not modelled. Glvi linker sequence (SQPARAA) substituted between Asp312-Asp401.,Includes an SBP tag at start of the sequence, this is not resolved in density and not modelled. Glvi linker sequence (SQPARAA) substituted between Asp312-Asp401.,Includes an SBP tag at start of the sequence, this is not resolved in density and not modelled. Glvi linker sequence (SQPARAA) substituted between Asp312-Asp401.,Includes an SBP tag at start of the sequence, this is not resolved in density and not modelled. Glvi linker sequence (SQPARAA) substituted between Asp312-Asp401.,Includes an SBP tag at start of the sequence, this is not resolved in density and not modelled. Glvi linker sequence (SQPARAA) substituted between Asp312-Asp401.,Includes an SBP tag at start of the sequence, this is not resolved in density and not modelled. Glvi linker sequence (SQPARAA) substituted between Asp312-Asp401.,Includes an SBP tag at start of the sequence, this is not resolved in density and not modelled. Glvi linker sequence (SQPARAA) substituted between Asp312-Asp401.,Includes an SBP tag at start of the sequence, this is not resolved in density and not modelled. Glvi linker sequence (SQPARAA) substituted between Asp312-Asp401.,Includes an SBP tag at start of the sequence, this is not resolved in density and not modelled. Glvi linker sequence (SQPARAA) substituted between Asp312-Asp401.,Includes an SBP tag at start of the sequence, this is not resolved in density and not modelled. Glvi linker sequence (SQPARAA) substituted between Asp312-Asp401.,Includes an SBP tag at start of the sequence, this is not resolved in density and not modelled. Glvi linker sequence (SQPARAA) substituted between Asp312-Asp401.,Includes an SBP tag at start of the sequence, this is not resolved in density and not modelled. Glvi linker sequence (SQPARAA) substituted between Asp312-Asp401.,Includes an SBP tag at start of the sequence, this is not resolved in density and not modelled. Glvi linker sequence (SQPARAA) substituted between Asp312-Asp401.,Includes an SBP tag at start of the sequence, this is not resolved in density and not modelled. Glvi linker sequence (SQPARAA) substituted between Asp312-Asp401.,Includes an SBP tag at start of the sequence, this is not resolved in density and not modelled. Glvi linker sequence (SQPARAA) substituted between Asp312-Asp401.,Includes an SBP tag at start of the sequence, this is not resolved in density and not modelled. Glvi linker sequence (SQPARAA) substituted between Asp312-Asp401.,Includes an SBP tag at start of the sequence, this is not resolved in density and not modelled. Glvi linker sequence (SQPARAA) substituted between Asp312-Asp401.,Includes an SBP tag at start of the sequence, this is not resolved in density and not modelled. Glvi linker sequence (SQPARAA) substituted between Asp312-Asp401.,Includes an SBP tag at start of the sequence, this is not resolved in density and not modelled. Glvi linker sequence (SQPARAA) substituted between Asp312-Asp401.,Includes an SBP tag at start of the sequence, this is not resolved in density and not modelled. Glvi linker sequence (SQPARAA) substituted between Asp312-Asp401.,Includes an SBP tag at start of the sequence, this is not resolved in density and not modelled. Glvi linker sequence (SQPARAA) substituted between Asp312-Asp401.,Includes an SBP tag at start of the sequence, this is not resolved in density and not modelled. Glvi linker sequence (SQPARAA) substituted between Asp312-Asp401.,Includes an SBP tag at start of the sequence, this is not resolved in density and not modelled. Glvi linker sequence (SQPARAA) substituted between Asp312-Asp401.,Includes an SBP tag at start of the sequence, this is not resolved in density and not modelled. Glvi linker sequence (SQPARAA) substituted between Asp312-Asp401.,Includes an SBP tag at start of the sequence, this is not resolved in density and not modelled. Glvi linker sequence (SQPARAA) substituted between Asp312-Asp401.,Includes an SBP tag at start of the sequence, this is not resolved in density and not modelled. Glvi linker sequence (SQPARAA) substituted between Asp312-Asp401.,Includes an SBP tag at start of the sequence, this is not resolved in density and not modelled. Glvi linker sequence (SQPARAA) substituted between Asp312-Asp401.,Includes an SBP tag at start of the sequence, this is not resolved in density and not modelled. Glvi linker sequence (SQPARAA) substituted between Asp312-Asp401.,Includes an SBP tag at start of the sequence, this is not resolved in density and not modelled. Glvi linker sequence (SQPARAA) substituted between Asp312-Asp401.
Source: (gene. exp.) Homo sapiens (human) / Gene: GABRD / Production host: Homo sapiens (human) / References: UniProt: O14764

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Antibody , 1 types, 2 molecules FG

#4: Antibody Nanobody Nb24


Mass: 13433.759 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Homo sapiens (human)

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Sugars , 3 types, 10 molecules

#5: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 383.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-Manp]{}}LINUCSPDB-CARE
#6: Polysaccharide beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-3DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b3-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(3+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#7: 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.: 8 / 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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Non-polymers , 4 types, 9 molecules

#8: Chemical
ChemComp-D10 / DECANE


Mass: 142.282 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H22
#9: Chemical ChemComp-PX6 / 1,2-DIPALMITOYL-SN-GLYCERO-3-PHOSPHATE


Mass: 647.883 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H68O8P
#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
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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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
1alpha4-beta3-delta GABA-A receptor in complex with GABA and nanobody Nb24COMPLEXThe heteropentameric alpha4beta3delta GABA(A) receptor was recombinantly expressed in Expi293 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 Nb24#1-#40MULTIPLE SOURCES
2GABA-A receptorCOMPLEX#1-#31RECOMBINANT
3Nanobody Nb24COMPLEX#41RECOMBINANT
Molecular weight
IDEntity assembly-IDExperimental value
11NO
21NO
31NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
32Homo sapiens (human)9606
53Lama glama (llama)9844
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDCellPlasmid
21Homo sapiens (human)9606
32Homo sapiens (human)9606Expi293F GnTI-pHLsec
53Homo sapiens (human)9606Expi293FpHLsec
Buffer solutionpH: 7.6
Details: 75 millimolar sodium chloride; 12.5 millimolar HEPES, pH 7.6; 10 millimolar biotin
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Nanodisc-reconstituted alpha4beta3delta GABA-A receptor in complex with GABA and nanobody Nb24
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid 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: 130000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1.44 sec. / Electron dose: 49.95 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 8038

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.4.1 to 4.7.1particle selection
4cryoSPARC4.4.1 to 4.7.1CTF correction
7UCSF ChimeraX1.8model fitting
9PHENIX1.20.1_4487model refinement
10cryoSPARC4.4.1 to 4.7.1initial Euler assignment
11cryoSPARC4.4.1 to 4.7.1final Euler assignment
12cryoSPARC4.4.1 to 4.7.1classification
13cryoSPARC4.4.1 to 4.7.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1606604
3D reconstructionResolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 47269 / Symmetry type: POINT
Atomic model buildingPDB-ID: 7QN7

7qn7


Accession code: 7QN7 / Source name: PDB / Type: experimental model
RefinementHighest resolution: 3.27 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00416015
ELECTRON MICROSCOPYf_angle_d0.52221734
ELECTRON MICROSCOPYf_dihedral_angle_d5.3122302
ELECTRON MICROSCOPYf_chiral_restr0.0432449
ELECTRON MICROSCOPYf_plane_restr0.0052693

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