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- EMDB-17636: Cryo-EM structure of the full-length human alpha1beta3 GABA(A) re... -

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Basic information

Entry
Database: EMDB / ID: EMD-17636
TitleCryo-EM structure of the full-length human alpha1beta3 GABA(A) receptor (babba arrangement) in complex with nanobody Nb25, expressed with a 5-fold excess of beta3 over alpha1
Map dataSharpened map aligned with the model
Sample
  • Complex: Cryo-EM structure of the full-length human alpha1beta3 GABA(A) receptor (babba arrangement) in complex with nanobody Nb25, expressed with a 5-fold excess of beta3 over alpha1
    • Protein or peptide: Gamma-aminobutyric acid receptor subunit alpha-1
    • Protein or peptide: Gamma-aminobutyric acid receptor subunit beta-3
    • Protein or peptide: Nanobody Nb25
  • Ligand: HEXADECANE
  • Ligand: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate
  • Ligand: DECANE
  • Ligand: ZINC ION
  • Ligand: water
KeywordsNeurotransmitter receptor / pentameric ligand-gated ion channel / Type-A GABA receptor / GABA-A receptor / MEMBRANE PROTEIN
Function / homology
Function and homology information


GABA receptor complex / cellular response to histamine / GABA receptor activation / GABA-A receptor activity / GABA-gated chloride ion channel activity / GABA-A receptor complex / inhibitory synapse assembly / postsynaptic specialization membrane / synaptic transmission, GABAergic / gamma-aminobutyric acid signaling pathway ...GABA receptor complex / cellular response to histamine / GABA receptor activation / GABA-A receptor activity / GABA-gated chloride ion channel activity / GABA-A receptor complex / inhibitory synapse assembly / postsynaptic specialization membrane / synaptic transmission, GABAergic / gamma-aminobutyric acid signaling pathway / roof of mouth development / Signaling by ERBB4 / chloride channel complex / dendrite membrane / cytoplasmic vesicle 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 / signal transduction / identical protein binding / plasma membrane
Similarity search - Function
Gamma-aminobutyric-acid A receptor, alpha 1 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 transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. ...Gamma-aminobutyric-acid A receptor, alpha 1 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 transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. / 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 alpha-1 / Gamma-aminobutyric acid receptor subunit beta-3
Similarity search - Component
Biological speciesHomo sapiens (human) / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsSente A / Malinauskas T / Naydenova K / Hardwick SW / Chirgadze DY / Aricescu AR
Funding support United Kingdom, United States, 5 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/L009609/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MC_UP_1201/15 United Kingdom
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM135550-01 United States
Medical Research Council (MRC, United Kingdom)MC_EX_MR/T046279/1 United Kingdom
National Science Foundation (NSF, United States)2014862 United States
CitationJournal: To Be Published
Title: Subunit abundance shapes GABAA receptor stoichiometry
Authors: Sente A / Malinauskas T / Naydenova K / Hardwick SW / Chirgadze DY / Aricescu AR
History
DepositionJun 14, 2023-
Header (metadata) releaseJul 2, 2025-
Map releaseJul 2, 2025-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17636.png

Downloads & links

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Map

FileDownload / File: emd_17636.map.gz / Format: CCP4 / Size: 93 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map aligned with the model
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.9 Å/pix.
x 290 pix.
= 259.84 Å		0.9 Å/pix.
x 290 pix.
= 259.84 Å		0.9 Å/pix.
x 290 pix.
= 259.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.896 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.004
Minimum - Maximum-1.9753102 - 3.0167594
Average (Standard dev.)0.005968393 (±0.07724681)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions290290290
Spacing290290290
CellA=B=C: 259.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_17636_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened map aligned with the model

Fileemd_17636_additional_1.map
AnnotationUnsharpened map aligned with the model
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_17636_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_17636_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of the full-length human alpha1beta3 GABA(A) re...

EntireName: Cryo-EM structure of the full-length human alpha1beta3 GABA(A) receptor (babba arrangement) in complex with nanobody Nb25, expressed with a 5-fold excess of beta3 over alpha1
Components
  • Complex: Cryo-EM structure of the full-length human alpha1beta3 GABA(A) receptor (babba arrangement) in complex with nanobody Nb25, expressed with a 5-fold excess of beta3 over alpha1
    • Protein or peptide: Gamma-aminobutyric acid receptor subunit alpha-1
    • Protein or peptide: Gamma-aminobutyric acid receptor subunit beta-3
    • Protein or peptide: Nanobody Nb25
  • Ligand: HEXADECANE
  • Ligand: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate
  • Ligand: DECANE
  • Ligand: ZINC ION
  • Ligand: water

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Supramolecule #1: Cryo-EM structure of the full-length human alpha1beta3 GABA(A) re...

SupramoleculeName: Cryo-EM structure of the full-length human alpha1beta3 GABA(A) receptor (babba arrangement) in complex with nanobody Nb25, expressed with a 5-fold excess of beta3 over alpha1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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

MacromoleculeName: Gamma-aminobutyric acid receptor subunit alpha-1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 54.100066 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGILPSPGMP ALLSLVSLLS VLLMGCVAET GWSHPQFEKG GGSGGGSGGS AWSHPQFEKG GSTGDNTTVF TRILDRLLDG YDNRLRPGL GERVTEVKTD IFVTSFGPVS DHDMEYTIDV FFRQSWKDER LKFKGPMTVL RLNNLMASKI WTPDTFFHNG K KSVAHNMT ...String:
MGILPSPGMP ALLSLVSLLS VLLMGCVAET GWSHPQFEKG GGSGGGSGGS AWSHPQFEKG GSTGDNTTVF TRILDRLLDG YDNRLRPGL GERVTEVKTD IFVTSFGPVS DHDMEYTIDV FFRQSWKDER LKFKGPMTVL RLNNLMASKI WTPDTFFHNG K KSVAHNMT MPNKLLRITE DGTLLYTMRL TVRAECPMHL EDFPMDAHAC PLKFGSYAYT RAEVVYEWTR EPARSVVVAE DG SRLNQYD LLGQTVDSGI VQSSTGEYVV MTTHFHLKRK IGYFVIQTYL PCIMTVILSQ VSFWLNRESV PARTVFGVTT VLT MTTLSI SARNSLPKVA YATAMDWFIA VCYAFVFSAL IEFATVNYFT KRGYAWDGKS VVPEKPKKVK DPLIKKNNTY APTA TSYTP NLARGDPGLA TIAKSATIEP KEVKPETKPP EPKKTFNSVS KIDRLSRIAF PLLFGIFNLV YWATYLNREP QLKAP TPHQ

UniProtKB: Gamma-aminobutyric acid receptor subunit alpha-1

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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 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 55.954316 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGILPSPGMP ALLSLVSLLS VLLMGCVAEY PYDVPDYATG QSVNDPGNMS FVKETVDKLL KGYDIRLRPD FGGPPVCVGM NIDIASIDM VSEVNMDYTL TMYFQQYWRD KRLAYSGIPL NLTLDNRVAD QLWVPDTYFL NDKKSFVHGV TVKNRMIRLH P DGTVLYGL ...String:
MGILPSPGMP ALLSLVSLLS VLLMGCVAEY PYDVPDYATG QSVNDPGNMS FVKETVDKLL KGYDIRLRPD FGGPPVCVGM NIDIASIDM VSEVNMDYTL TMYFQQYWRD KRLAYSGIPL NLTLDNRVAD QLWVPDTYFL NDKKSFVHGV TVKNRMIRLH P DGTVLYGL RITTTAACMM DLRRYPLDEQ NCTLEIESYG YTTDDIEFYW RGGDKAVTGV ERIELPQFSI VEHRLVSRNV VF ATGAYPR LSLSFRLKRN IGYFILQTYM PSILITILSW VSFWINYDAS AARVALGITT VLTMTTINTH LRETLPKIPY VKA IDMYLM GCFVFVFLAL LEYAFVNYIF FGRGPQRQKK LAEKTAKAKN DRSKSESNRV DAHGNILLTS LEVHNEMNEV SGGI GDTRN SAISFDNSGI QYRKQSMPRE GHGRFLGDRS LPHKKGTTHL RRRSSQLKIK IPDLTDVNAI DRWSRIVFPF TFSLF NLVY WLYYVN

UniProtKB: Gamma-aminobutyric acid receptor subunit beta-3

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Macromolecule #3: Nanobody Nb25

MacromoleculeName: Nanobody Nb25 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 14.928326 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
QVQLQESGGG LVQAGGSLRL SCAASGHTFN YPIMGWFRQA PGKEREFVGA ISWSGGSTSY ADSVKDRFTI SRDNAKNTVY LEMNNLKPE DTAVYYCAAK GRYSGGLYYP TNYDYWGQGT QVTVSSHHHH HHEPEA

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Macromolecule #6: HEXADECANE

MacromoleculeName: HEXADECANE / type: ligand / ID: 6 / Number of copies: 2 / Formula: R16
Molecular weightTheoretical: 226.441 Da
Chemical component information

ChemComp-R16:
HEXADECANE

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Macromolecule #7: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(o...

MacromoleculeName: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate
type: ligand / ID: 7 / Number of copies: 2 / Formula: PIO
Molecular weightTheoretical: 746.566 Da
Chemical component information

ChemComp-PIO:
[(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate

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Macromolecule #8: DECANE

MacromoleculeName: DECANE / type: ligand / ID: 8 / Number of copies: 12 / Formula: D10
Molecular weightTheoretical: 142.282 Da
Chemical component information

ChemComp-D10:
DECANE

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Macromolecule #9: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 9 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #10: water

MacromoleculeName: water / type: ligand / ID: 10 / Number of copies: 84 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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
Component:
ConcentrationFormulaName
300.0 mMNaClsodium chloride
50.0 mMHEPES
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 287 K / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 10020 / Average electron dose: 50.63 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 130000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2175702
CTF correctionSoftware - Name: CTFFIND (ver. 4.1.13) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: AB INITIO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1.2) / Number images used: 213401
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1.2)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-8pet:
Cryo-EM structure of the full-length human alpha1beta3 GABA(A) receptor (babba arrangement) in complex with nanobody Nb25, expressed with a 5-fold excess of beta3 over alpha1

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