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- EMDB-50280: CryoEM structure of human full-length alpha1beta3gamma2L GABA(A)R... -

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Basic information

Entry
Database: EMDB / ID: EMD-50280
TitleCryoEM structure of human full-length alpha1beta3gamma2L GABA(A)R in complex with pregnenolone sulfate
Map dataPostprocessed map
Sample
  • Complex: CryoEM structure of human full-length alpha1beta3gamma2L GABA(A)R in complex with pregnenolone sulfate
    • Protein or peptide: x 3 types
  • Ligand: x 11 types
KeywordsGABA / Neurotransmission / Ternary complex / Inhibitory synapse / Neurosteroid / MEMBRANE PROTEIN
Function / homology
Function and homology information


benzodiazepine receptor activity / 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 / gamma-aminobutyric acid signaling pathway / postsynaptic specialization membrane ...benzodiazepine receptor activity / 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 / gamma-aminobutyric acid signaling pathway / postsynaptic specialization membrane / synaptic transmission, GABAergic / chloride channel activity / adult behavior / roof of mouth development / Signaling by ERBB4 / chloride channel complex / dendrite membrane / cytoplasmic vesicle membrane / chloride transmembrane transport / post-embryonic development / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / GABA-ergic synapse / dendritic spine / postsynaptic membrane / postsynapse / axon / signal transduction / identical protein binding / plasma membrane
Similarity search - Function
Gamma-aminobutyric-acid A receptor, gamma 2 subunit / Gamma-aminobutyric acid receptor subunit gamma-1/4 / 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 ...Gamma-aminobutyric-acid A receptor, gamma 2 subunit / Gamma-aminobutyric acid receptor subunit gamma-1/4 / 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 gamma-2 / Gamma-aminobutyric acid receptor subunit beta-3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsKasaragod VB / Aricescu AR
Funding support United Kingdom, European Union, United States, 7 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UP_1201/15 United Kingdom
European Molecular Biology Organization (EMBO)ALTF137-2019European Union
H2020 Marie Curie Actions of the European CommissionGABAARComp-897707European Union
Medical Research Council (MRC, United Kingdom)MR/L009609/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MC_EX_MR/T046279/1 United Kingdom
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01-GM135550 United States
National Science Foundation (NSF, United States)NeuroNex 2014862 United States
CitationJournal: To Be Published
Title: CryoEM structure of human full-length alpha1beta3gamma2L GABA(A)R in complex with pregnenolone sulfate
Authors: Kasaragod VB / Aricescu AR
History
DepositionMay 10, 2024-
Header (metadata) releaseMay 28, 2025-
Map releaseMay 28, 2025-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50280.png

Downloads & links

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Map

FileDownload / File: emd_50280.map.gz / Format: CCP4 / Size: 320.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPostprocessed map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 438 pix.
= 360.912 Å		0.82 Å/pix.
x 438 pix.
= 360.912 Å		0.82 Å/pix.
x 438 pix.
= 360.912 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.824 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.28
Minimum - Maximum-0.99071085 - 2.086431
Average (Standard dev.)0.0011294809 (±0.03330167)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions438438438
Spacing438438438
CellA=B=C: 360.912 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_50280_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened map

Fileemd_50280_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: One of the halfmaps

Fileemd_50280_half_map_1.map
AnnotationOne of the halfmaps
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: One of the halfmaps

Fileemd_50280_half_map_2.map
AnnotationOne of the halfmaps
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : CryoEM structure of human full-length alpha1beta3gamma2L GABA(A)R...

EntireName: CryoEM structure of human full-length alpha1beta3gamma2L GABA(A)R in complex with pregnenolone sulfate
Components
  • Complex: CryoEM structure of human full-length alpha1beta3gamma2L GABA(A)R in complex with pregnenolone sulfate
    • Protein or peptide: Gamma-aminobutyric acid receptor subunit alpha-1
    • Protein or peptide: Gamma-aminobutyric acid receptor subunit beta-3
    • Protein or peptide: Isoform 1 of Gamma-aminobutyric acid receptor subunit gamma-2
  • Ligand: HEXANE
  • 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: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate
  • Ligand: DECANE
  • Ligand: PALMITIC ACID
  • Ligand: CHLORIDE ION
  • Ligand: 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE
  • Ligand: HEXADECANE
  • Ligand: Pregnenolone sulfate
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water

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Supramolecule #1: CryoEM structure of human full-length alpha1beta3gamma2L GABA(A)R...

SupramoleculeName: CryoEM structure of human full-length alpha1beta3gamma2L GABA(A)R in complex with pregnenolone sulfate
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 400 KDa

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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: 46.585602 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DNTTVFTRIL DRLLDGYDNR LRPGLGERVT EVKTDIFVTS FGPVSDHDME YTIDVFFRQS WKDERLKFKG PMTVLRLNNL MASKIWTPD TFFHNGKKSV AHNMTMPNKL LRITEDGTLL YTMRLTVRAE CPMHLEDFPM DAHACPLKFG SYAYTRAEVV Y EWTREPAR ...String:
DNTTVFTRIL DRLLDGYDNR LRPGLGERVT EVKTDIFVTS FGPVSDHDME YTIDVFFRQS WKDERLKFKG PMTVLRLNNL MASKIWTPD TFFHNGKKSV AHNMTMPNKL LRITEDGTLL YTMRLTVRAE CPMHLEDFPM DAHACPLKFG SYAYTRAEVV Y EWTREPAR SVVVAEDGSR LNQYDLLGQT VDSGIVQSST GEYVVMTTHF HLKRKIGYFV IQTYLPCIMT VILSQVSFWL NR ESVPART VFGVTTVLTM TTLSISARNS LPKVAYATAM DWFIAVCYAF VFSALIEFAT VNYFTKRGYA WDGKSVVPEK PKK VKDPLI KKNNTYAPTA TSYTPNLARG DPGLATIAKS ATIEPKEVKP ETKPPEPKKT FNSVSKIDRL SRIAFPLLFG IFNL VYWAT YLNR

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: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 50.904527 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GNMSFVKETV DKLLKGYDIR LRPDFGGPPV CVGMNIDIAS IDMVSEVNMD YTLTMYFQQY WRDKRLAYSG IPLNLTLDNR VADQLWVPD TYFLNDKKSF VHGVTVKNRM IRLHPDGTVL YGLRITTTAA CMMDLRRYPL DEQNCTLEIE SYGYTTDDIE F YWRGGDKA ...String:
GNMSFVKETV DKLLKGYDIR LRPDFGGPPV CVGMNIDIAS IDMVSEVNMD YTLTMYFQQY WRDKRLAYSG IPLNLTLDNR VADQLWVPD TYFLNDKKSF VHGVTVKNRM IRLHPDGTVL YGLRITTTAA CMMDLRRYPL DEQNCTLEIE SYGYTTDDIE F YWRGGDKA VTGVERIELP QFSIVEHRLV SRNVVFATGA YPRLSLSFRL KRNIGYFILQ TYMPSILITI LSWVSFWINY DA SAARVAL GITTVLTMTT INTHLRETLP KIPYVKAIDM YLMGCFVFVF LALLEYAFVN YIFFGRGPQR QKKLAEKTAK AKN DRSKSE SNRVDAHGNI LLTSLEVHNE MNEVSGGIGD TRNSAISFDN SGIQYRKQSM PREGHGRFLG DRSLPHKKTH LRRR SSQLK IKIPDLTDVN AIDRWSRIVF PFTFSLFNLV YWLYYV

UniProtKB: Gamma-aminobutyric acid receptor subunit beta-3

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Macromolecule #3: Isoform 1 of Gamma-aminobutyric acid receptor subunit gamma-2

MacromoleculeName: Isoform 1 of Gamma-aminobutyric acid receptor subunit gamma-2
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 48.123426 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GDVTVILNNL LEGYDNKLRP DIGVKPTLIH TDMYVNSIGP VNAINMEYTI DIFFAQTWYD RRLKFNSTIK VLRLNSNMVG KIWIPDTFF RNSKKADAHW ITTPNRMLRI WNDGRVLYTL RLTIDAECQL QLHNFPMDEH SCPLEFSSYG YPREEIVYQW K RSSVEVGD ...String:
GDVTVILNNL LEGYDNKLRP DIGVKPTLIH TDMYVNSIGP VNAINMEYTI DIFFAQTWYD RRLKFNSTIK VLRLNSNMVG KIWIPDTFF RNSKKADAHW ITTPNRMLRI WNDGRVLYTL RLTIDAECQL QLHNFPMDEH SCPLEFSSYG YPREEIVYQW K RSSVEVGD TRSWRLYQFS FVGLRNTTEV VKTTSGDYVV MSVYFDLSRR MGYFTIQTYI PCTLIVVLSW VSFWINKDAV PA RTSLGIT TVLTMTTLST IARKSLPKVS YVTAMDLFVS VCFIFVFSAL VEYGTLHYFV SNRKPSKDKD KKKKNPLLRM FSF KAPTID IRPRSATIQM NNATHLQERD EEYGYECLDG KDCASFFCCF EDCRTGAWRH GRIHIRIAKM DSYARIFFPT AFCL FNLVY WVSYLYL

UniProtKB: Gamma-aminobutyric acid receptor subunit gamma-2

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Macromolecule #8: HEXANE

MacromoleculeName: HEXANE / type: ligand / ID: 8 / Number of copies: 8 / Formula: HEX
Molecular weightTheoretical: 86.175 Da
Chemical component information

ChemComp-HEX:
HEXANE

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Macromolecule #9: [(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: 9 / 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 #10: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]o...

MacromoleculeName: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate
type: ligand / ID: 10 / Number of copies: 3 / Formula: PGW
Molecular weightTheoretical: 749.007 Da

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Macromolecule #11: DECANE

MacromoleculeName: DECANE / type: ligand / ID: 11 / Number of copies: 17 / Formula: D10
Molecular weightTheoretical: 142.282 Da
Chemical component information

ChemComp-D10:
DECANE

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Macromolecule #12: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 12 / Number of copies: 3 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID

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Macromolecule #13: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 13 / Number of copies: 3 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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Macromolecule #14: 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE

MacromoleculeName: 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE / type: ligand / ID: 14 / Number of copies: 1 / Formula: PX2
Molecular weightTheoretical: 535.671 Da
Chemical component information

ChemComp-PX2:
1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE

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Macromolecule #15: HEXADECANE

MacromoleculeName: HEXADECANE / type: ligand / ID: 15 / Number of copies: 5 / Formula: R16
Molecular weightTheoretical: 226.441 Da
Chemical component information

ChemComp-R16:
HEXADECANE

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Macromolecule #16: Pregnenolone sulfate

MacromoleculeName: Pregnenolone sulfate / type: ligand / ID: 16 / Number of copies: 1 / Formula: A8W
Molecular weightTheoretical: 396.541 Da
Chemical component information

ChemComp-A8W:
Pregnenolone sulfate / antidepressant*YM

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Macromolecule #17: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 17 / Number of copies: 1 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #18: water

MacromoleculeName: water / type: ligand / ID: 18 / Number of copies: 303 / 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

Concentration1 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
15.0 mMHEPES4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
150.0 mMNaClSodium chloride

Details: 15 mM Hepes pH 7.4, 150 mM NaCl
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa / Details: Current: 30 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 287 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Digitization - Dimensions - Width: 4098 pixel / Digitization - Dimensions - Height: 4098 pixel / Number grids imaged: 1 / Number real images: 12363 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 96000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 96000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1886351
CTF correctionSoftware - Name: CTFFIND (ver. 4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab-initio model
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.40) / Number images used: 86252
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.40)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.40)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.40)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6huk


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: OTHER / Overall B value: 30 / Target criteria: FSC at 0.5
Output model

PDB-9fas:
CryoEM structure of human full-length alpha1beta3gamma2L GABA(A)R in complex with pregnenolone sulfate

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