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- EMDB-55007: GABA-A a4b3d receptor in complex with GABA and Nb24 -

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Basic information

Entry
Database: EMDB / ID: EMD-55007
TitleGABA-A a4b3d receptor in complex with GABA and Nb24
Map data
Sample
  • Complex: alpha4-beta3-delta GABA-A receptor in complex with GABA and nanobody Nb24
    • Complex: GABA-A receptor
      • Protein or peptide: Gamma-aminobutyric acid receptor subunit alpha-4,Gamma-aminobutyric acid type A receptor subunit alpha4
      • Protein or peptide: Gamma-aminobutyric acid receptor subunit beta-3
      • Protein or peptide: Gamma-aminobutyric acid receptor subunit delta
    • Complex: Nanobody Nb24
      • Protein or peptide: Nanobody Nb24
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: DECANE
  • Ligand: 1,2-DIPALMITOYL-SN-GLYCERO-3-PHOSPHATE
  • Ligand: GAMMA-AMINO-BUTANOIC ACID
  • Ligand: water
KeywordspLGIC / GABA / Neurotransmission / Extrasynaptic / MEMBRANE PROTEIN
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-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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.27 Å
AuthorsNestorow S / Miller PS
Funding support United Kingdom, Switzerland, 2 items
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 SA / Chen WN / Bertrand D / Wahid AA / Wyatt CE / Mortensen M / Clairfeuille T / Reutlinger M / Friz G / Pardon E / Steyaert J / Ladds G / Cecere G / Smart TG / Hernandez MC / Joedicke L / Miller PS
History
DepositionSep 4, 2025-
Header (metadata) releaseSep 2, 2026-
Map releaseSep 2, 2026-
UpdateSep 2, 2026-
Current statusSep 2, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55007.png

Downloads & links

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Map

FileDownload / File: emd_55007.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.
= 247.68 Å		0.65 Å/pix.
x 384 pix.
= 247.68 Å		0.65 Å/pix.
x 384 pix.
= 247.68 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.645 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0559
Minimum - Maximum-0.13403425 - 0.22511081
Average (Standard dev.)0.0008200048 (±0.008717507)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 247.68 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_55007_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_55007_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_55007_half_map_2.map
Projections & Slices
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Sample components

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Entire : alpha4-beta3-delta GABA-A receptor in complex with GABA and nanob...

EntireName: alpha4-beta3-delta GABA-A receptor in complex with GABA and nanobody Nb24
Components
  • Complex: alpha4-beta3-delta GABA-A receptor in complex with GABA and nanobody Nb24
    • Complex: GABA-A receptor
      • Protein or peptide: Gamma-aminobutyric acid receptor subunit alpha-4,Gamma-aminobutyric acid type A receptor subunit alpha4
      • Protein or peptide: Gamma-aminobutyric acid receptor subunit beta-3
      • Protein or peptide: Gamma-aminobutyric acid receptor subunit delta
    • Complex: Nanobody Nb24
      • Protein or peptide: Nanobody Nb24
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: DECANE
  • Ligand: 1,2-DIPALMITOYL-SN-GLYCERO-3-PHOSPHATE
  • Ligand: GAMMA-AMINO-BUTANOIC ACID
  • Ligand: water

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Supramolecule #1: alpha4-beta3-delta GABA-A receptor in complex with GABA and nanob...

SupramoleculeName: alpha4-beta3-delta GABA-A receptor in complex with GABA and nanobody Nb24
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Details: The 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 ...Details: The 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
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 Nb24

SupramoleculeName: Nanobody Nb24 / 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-4,Gamma-aminobutyr...

MacromoleculeName: Gamma-aminobutyric acid receptor subunit alpha-4,Gamma-aminobutyric acid type A receptor subunit alpha4
type: protein_or_peptide / ID: 1
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.
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.783336 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GNSKDEKLCP ENFTRILDSL LDGYDNRLRP GFGGPVTEVK TDIYVTSFGP VSDVEMEYTM DVFFRQTWID KRLKYDGPIE ILRLNNMMV TKVWTPDTFF RNGKKSVSHN MTAPNKLFRI TRNGTILYTM RLTISAECPM RLVDFPMDGH ACPLKFGSYA Y PKSEMIYT ...String:
GNSKDEKLCP ENFTRILDSL LDGYDNRLRP GFGGPVTEVK TDIYVTSFGP VSDVEMEYTM DVFFRQTWID KRLKYDGPIE ILRLNNMMV TKVWTPDTFF RNGKKSVSHN MTAPNKLFRI TRNGTILYTM RLTISAECPM RLVDFPMDGH ACPLKFGSYA Y PKSEMIYT WTKGPEKSVE VPKESSSLVQ YDLIGQTVSS ETIKSITGEY IVMTVYFHLR RKMGYFMIQT YIPCIMTVIL SQ VSFWINK ESVPARTVFG ITTVLTMTTL SISARHSLPK VSYATAMDWF IAVCFAFVFS ALIEFAAVNY FTNSQPARAA KID KYARIL FPVTFGAFNM VYWVVYLSKD TMEKSESLMG TKHHHHHH

UniProtKB: Gamma-aminobutyric acid receptor subunit alpha-4, Gamma-aminobutyric acid type A receptor subunit alpha4

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

MacromoleculeName: Gamma-aminobutyric acid receptor subunit beta-3 / 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.,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.
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, Gamma-aminobutyric acid receptor subunit beta-3

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Macromolecule #3: Gamma-aminobutyric acid receptor subunit delta

MacromoleculeName: Gamma-aminobutyric acid receptor subunit delta / type: protein_or_peptide / ID: 3
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.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 48.233961 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGILPSPGMP ALLSLVSLLS VLLMGCVAEM DEKTTGWRGG HVVEGLAGEL EQLRARLEHH PQGQREPDYD IPTTENLYFQ GTGAMNDIG DYVGSNLEIS WLPNLDGLIA GYARNFRPGI GGPPVNVALA LEVASIDHIS EANMEYTMTV FLHQSWRDSR L SYNHTNET ...String:
MGILPSPGMP ALLSLVSLLS VLLMGCVAEM DEKTTGWRGG HVVEGLAGEL EQLRARLEHH PQGQREPDYD IPTTENLYFQ GTGAMNDIG DYVGSNLEIS WLPNLDGLIA GYARNFRPGI GGPPVNVALA LEVASIDHIS EANMEYTMTV FLHQSWRDSR L SYNHTNET LGLDSRFVDK LWLPDTFIVN AKSAWFHDVT VENKLIRLQP DGVILYSIRI TSTVACDMDL AKYPMDEQEC ML DLESYGY SSEDIVYYWS ESQEHIHGLD KLQLAQFTIT SYRFTTELMN FKSAGQFPRL SLHFHLRRNR GVYIIQSYMP SVL LVAMSW VSFWISQAAV PARVSLGITT VLTMTTLMVS ARSSLPRASA IKALDVYFWI CYVFVFAALV EYAFAHFNAD SQPA RAATI DIYARAVFPA AFAAVNVIYW AAYAM

UniProtKB: Gamma-aminobutyric acid receptor subunit delta, Gamma-aminobutyric acid receptor subunit delta

+
Macromolecule #4: Nanobody Nb24

MacromoleculeName: Nanobody Nb24 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 13.433759 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLQESGGG LVQAGDSLRL SCAASGRSIR NYHMGWFRQA PGKERDFVAA ILWSGSSTFY ADSVKGRFTV SRDNAKNTVY LQMNSLKPE DTAVYYCALH RGGSEDSPQA YDSWGQGTQV TVSS

+
Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 8 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

+
Macromolecule #8: DECANE

MacromoleculeName: DECANE / type: ligand / ID: 8 / Number of copies: 4 / Formula: D10
Molecular weightTheoretical: 142.282 Da
Chemical component information

ChemComp-D10:
DECANE

+
Macromolecule #9: 1,2-DIPALMITOYL-SN-GLYCERO-3-PHOSPHATE

MacromoleculeName: 1,2-DIPALMITOYL-SN-GLYCERO-3-PHOSPHATE / type: ligand / ID: 9 / Number of copies: 1 / Formula: PX6
Molecular weightTheoretical: 647.883 Da
Chemical component information

ChemComp-PX6:
1,2-DIPALMITOYL-SN-GLYCERO-3-PHOSPHATE

+
Macromolecule #10: GAMMA-AMINO-BUTANOIC ACID

MacromoleculeName: GAMMA-AMINO-BUTANOIC ACID / type: ligand / ID: 10 / Number of copies: 2 / Formula: ABU
Molecular weightTheoretical: 103.12 Da
Chemical component information

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

+
Macromolecule #11: water

MacromoleculeName: water / type: ligand / ID: 11 / Number of copies: 2 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.6
Details: 75 millimolar sodium chloride; 12.5 millimolar HEPES, pH 7.6; 10 millimolar biotin
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 alpha4beta3delta GABA-A receptor in complex with GABA and nanobody Nb24

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 8038 / Average exposure time: 1.44 sec. / Average electron dose: 49.95 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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

+
Image processing

Particle selectionNumber selected: 1606604
CTF correctionSoftware - Name: cryoSPARC (ver. 4.4.1 to 4.7.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
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 reconstructionResolution.type: BY AUTHOR / Resolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1 to 4.7.1) / Number images used: 47269
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)

-
Atomic model buiding 1

Initial modelPDB ID:

7qn7


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

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

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