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- EMDB-50285: CryoEM structure of human full-length beta3gamma2 GABA(A) recepto... -

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Entry
Database: EMDB / ID: EMD-50285
TitleCryoEM structure of human full-length beta3gamma2 GABA(A) receptor in complex with Megabody25, doubly occupied GARLH4 and Neuroligin2 TMD, in a closed state
Map dataUnsharpened map
Sample
  • Complex: CryoEM structure of human full-length beta3gamma2 GABA(A) receptor in complex with Megabody25, doubly occupied GARLH4 and Neuroligin2 TMD, in a closed state
    • Protein or peptide: x 5 types
  • Ligand: x 8 types
KeywordsGABA / Neurotransmission / Ternary complex / Inhibitory synapse / MEMBRANE PROTEIN
Function / homology
Function and homology information


regulation of inhibitory synapse assembly / symmetric, GABA-ergic, inhibitory synapse / jump response / neurotransmitter-gated ion channel clustering / positive regulation of t-SNARE clustering / gephyrin clustering involved in postsynaptic density assembly / terminal button organization / postsynaptic density protein 95 clustering / positive regulation of synaptic vesicle clustering / postsynaptic membrane assembly ...regulation of inhibitory synapse assembly / symmetric, GABA-ergic, inhibitory synapse / jump response / neurotransmitter-gated ion channel clustering / positive regulation of t-SNARE clustering / gephyrin clustering involved in postsynaptic density assembly / terminal button organization / postsynaptic density protein 95 clustering / positive regulation of synaptic vesicle clustering / postsynaptic membrane assembly / gamma-aminobutyric acid receptor clustering / cell-cell junction maintenance / presynaptic membrane assembly / neurexin family protein binding / postsynaptic specialization / presynapse assembly / thigmotaxis / neuron cell-cell adhesion / insulin metabolic process / regulation of respiratory gaseous exchange by nervous system process / inhibitory synapse / benzodiazepine receptor activity / ribbon synapse / circadian sleep/wake cycle, REM sleep / reproductive behavior / protein localization to synapse / GABA receptor binding / dopaminergic synapse / hard palate development / positive regulation of inhibitory postsynaptic potential / cellular response to histamine / glycinergic synapse / GABA receptor activation / inner ear receptor cell development / inhibitory synapse assembly / GABA-A receptor activity / GABA-gated chloride ion channel activity / GABA-A receptor complex / innervation / protein localization to cell surface / positive regulation of synapse assembly / Neurexins and neuroligins / response to anesthetic / neuromuscular process controlling balance / postsynaptic specialization membrane / inhibitory postsynaptic potential / positive regulation of protein localization to synapse / neurotransmitter receptor localization to postsynaptic specialization membrane / gamma-aminobutyric acid signaling pathway / positive regulation of dendritic spine development / synaptic transmission, GABAergic / cellular response to zinc ion / exploration behavior / chloride channel activity / motor behavior / adult behavior / locomotory exploration behavior / roof of mouth development / Signaling by ERBB4 / cochlea development / excitatory synapse / social behavior / regulation of presynapse assembly / positive regulation of excitatory postsynaptic potential / positive regulation of synaptic transmission, glutamatergic / chloride channel complex / cell adhesion molecule binding / synapse assembly / sensory perception of pain / dendrite membrane / cytoplasmic vesicle membrane / chloride transmembrane transport / cerebellum development / dendritic shaft / post-embryonic development / positive regulation of synaptic transmission, GABAergic / learning / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / sensory perception of sound / cell-cell adhesion / synapse organization / modulation of chemical synaptic transmission / positive regulation of insulin secretion / GABA-ergic synapse / memory / presynaptic membrane / dendritic spine / postsynaptic membrane / postsynapse / response to xenobiotic stimulus / axon / positive regulation of cell population proliferation / synapse / dendrite / cell surface / signal transduction / identical protein binding / membrane / plasma membrane
Similarity search - Function
Lipoma HMGIC fusion partner-like protein / Lipoma HMGIC fusion partner-like protein / Neuroligin / : / Gamma-aminobutyric-acid A receptor, gamma 2 subunit / Gamma-aminobutyric acid receptor subunit gamma-1/4 / Gamma-aminobutyric-acid A receptor, beta subunit / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase, type B ...Lipoma HMGIC fusion partner-like protein / Lipoma HMGIC fusion partner-like protein / Neuroligin / : / Gamma-aminobutyric-acid A receptor, gamma 2 subunit / Gamma-aminobutyric acid receptor subunit gamma-1/4 / Gamma-aminobutyric-acid A receptor, beta subunit / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase, type B / Carboxylesterase family / 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 / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Gamma-aminobutyric acid receptor subunit gamma-2 / Gamma-aminobutyric acid receptor subunit beta-3 / LHFPL tetraspan subfamily member 4 protein / Neuroligin-2
Similarity search - Component
Biological speciesHomo sapiens (human) / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 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 beta3gamma2 GABA(A) receptor in complex with Megabody25, doubly occupied GARLH4 and Neuroligin2 TMD, in a closed state
Authors: Kasaragod VB / Aricescu AR
History
DepositionMay 10, 2024-
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

Downloads & links

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Map

FileDownload / File: emd_50285.map.gz / Format: CCP4 / Size: 381.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnsharpened map
Voxel sizeX=Y=Z: 0.729 Å
Density
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.3329309 - 0.725908
Average (Standard dev.)0.0023831856 (±0.017399466)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions464464464
Spacing464464464
CellA=B=C: 338.25598 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : CryoEM structure of human full-length beta3gamma2 GABA(A) recepto...

EntireName: CryoEM structure of human full-length beta3gamma2 GABA(A) receptor in complex with Megabody25, doubly occupied GARLH4 and Neuroligin2 TMD, in a closed state
Components
  • Complex: CryoEM structure of human full-length beta3gamma2 GABA(A) receptor in complex with Megabody25, doubly occupied GARLH4 and Neuroligin2 TMD, in a closed state
    • Protein or peptide: Isoform 2 of Gamma-aminobutyric acid receptor subunit gamma-2
    • Protein or peptide: Neuroligin-2
    • Protein or peptide: LHFPL tetraspan subfamily member 4 protein
    • Protein or peptide: Gamma-aminobutyric acid receptor subunit beta-3
    • Protein or peptide: Megabody25
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: HEXADECANE
  • Ligand: 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE
  • Ligand: CHOLESTEROL
  • Ligand: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate
  • Ligand: HEXANE
  • Ligand: DECANE
  • Ligand: PALMITIC ACID

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Supramolecule #1: CryoEM structure of human full-length beta3gamma2 GABA(A) recepto...

SupramoleculeName: CryoEM structure of human full-length beta3gamma2 GABA(A) receptor in complex with Megabody25, doubly occupied GARLH4 and Neuroligin2 TMD, in a closed state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 400 KDa

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

MacromoleculeName: Isoform 2 of Gamma-aminobutyric acid receptor subunit gamma-2
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 47.870398 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 KKKKNPAPTI DIR PRSATI QMNNATHLQE RDEEYGYECL DGKDCASFF(P1L) (P1L)FED(P1L)RTGAW RHGRIHIRIA KMDSYARIFF PT AFCLFNL VYWVSYLYLG

UniProtKB: Gamma-aminobutyric acid receptor subunit gamma-2

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Macromolecule #2: Neuroligin-2

MacromoleculeName: Neuroligin-2 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 3.614107 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DSRDYSTELS VTVAVGASLL FLNILAFAAL YYK

UniProtKB: Neuroligin-2

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Macromolecule #3: LHFPL tetraspan subfamily member 4 protein

MacromoleculeName: LHFPL tetraspan subfamily member 4 protein / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.634434 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MRNSRAIGVL WAIFTICFAI INVVVFIQPY WVGDSVSTPK PGYFGLFHYC VGSGLAGREL TCRGSFTDFS TIPSSAFKAA AFFVLLSMV LILGCITCFS LFFFCNTATV YKICAWMQLL AALCLVLGCM IFPDGWDAET IRDMCGAKTG KYSLGDCSVR W AYILAIIG ILNALILSFL AFVLGNRQTD

UniProtKB: LHFPL tetraspan subfamily member 4 protein

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Macromolecule #4: Gamma-aminobutyric acid receptor subunit beta-3

MacromoleculeName: Gamma-aminobutyric acid receptor subunit beta-3 / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 50.733375 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSFVKETVDK LLKGYDIRLR PDFGGPPVCV GMNIDIASID MVSEVNMDYT LTMYFQQYWR DKRLAYSGIP LNLTLDNRVA DQLWVPDTY FLNDKKSFVH GVTVKNRMIR LHPDGTVLYG LRITTTAACM MDLRRYPLDE QNCTLEIESY GYTTDDIEFY W RGGDKAVT ...String:
MSFVKETVDK LLKGYDIRLR PDFGGPPVCV GMNIDIASID MVSEVNMDYT LTMYFQQYWR DKRLAYSGIP LNLTLDNRVA DQLWVPDTY FLNDKKSFVH GVTVKNRMIR LHPDGTVLYG LRITTTAACM MDLRRYPLDE QNCTLEIESY GYTTDDIEFY W RGGDKAVT GVERIELPQF SIVEHRLVSR NVVFATGAYP RLSLSFRLKR NIGYFILQTY MPSILITILS WVSFWINYDA SA ARVALGI TTVLTMTTIN THLRETLPKI PYVKAIDMYL MGCFVFVFLA LLEYAFVNYI FFGRGPQRQK KLAEKTAKAK NDR SKSESN RVDAHGNILL TSLEVHNEMN EVSGGIGDTR NSAISFDNSG IQYRKQSMPR EGHGRFLGDR SLPHKKTHLR RRSS QLKIK IPDLTDVNAI DRWSRIVFPF TFSLFNLVYW LYYV

UniProtKB: Gamma-aminobutyric acid receptor subunit beta-3

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Macromolecule #5: Megabody25

MacromoleculeName: Megabody25 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 56.300629 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: QVQLVESGGG LVQTKTTTSV IDTTNDAQNL LTQAQTIVNT LKDYCPILIA KSSSSNGGTN NANTPSWQTA GGGKNSCATF GAEFSAASD MINNAQKIVQ ETQQLSANQP KNITQPHNLN LNSPSSLTAL AQKMLKNAQS QAEILKLANQ VESDFNKLSS G HLKDYIGK ...String:
QVQLVESGGG LVQTKTTTSV IDTTNDAQNL LTQAQTIVNT LKDYCPILIA KSSSSNGGTN NANTPSWQTA GGGKNSCATF GAEFSAASD MINNAQKIVQ ETQQLSANQP KNITQPHNLN LNSPSSLTAL AQKMLKNAQS QAEILKLANQ VESDFNKLSS G HLKDYIGK CDASAISSAN MTMQNQKNNW GNGCAGVEET QSLLKTSAAD FNNQTPQINQ AQNLANTLIQ ELGNNTYEQL SR LLTNDNG TNSKTSAQAI NQAVNNLNER AKTLAGGTTN SPAYQATLLA LRSVLGLWNS MGYAVICGGY TKSPGENNQK DFH YTDENG NGTTINCGGS TNSNGTHSYN GTNTLKADKN VSLSIEQYEK IHEAYQILSK ALKQAGLAPL NSKGEKLEAH VTTS KYGSL RLSCAASGHT FNYPIMGWFR QAPGKEREFV GAISWSGGST SYADSVKDRF TISRDNAKNT VYLEMNNLKP EDTAV YYCA AKGRYSGGLY YPTNYDYWGQ GTQVTVSSHH HHHHEPEA

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Macromolecule #11: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 11 / Number of copies: 2 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #12: HEXADECANE

MacromoleculeName: HEXADECANE / type: ligand / ID: 12 / Number of copies: 5 / Formula: R16
Molecular weightTheoretical: 226.441 Da
Chemical component information

ChemComp-R16:
HEXADECANE

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Macromolecule #13: 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE

MacromoleculeName: 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE / type: ligand / ID: 13 / Number of copies: 2 / Formula: PX2
Molecular weightTheoretical: 535.671 Da
Chemical component information

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

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Macromolecule #14: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 14 / Number of copies: 2 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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Macromolecule #15: (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: 15 / Number of copies: 4 / Formula: PGW
Molecular weightTheoretical: 749.007 Da

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Macromolecule #16: HEXANE

MacromoleculeName: HEXANE / type: ligand / ID: 16 / Number of copies: 13 / Formula: HEX
Molecular weightTheoretical: 86.175 Da
Chemical component information

ChemComp-HEX:
HEXANE

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Macromolecule #17: DECANE

MacromoleculeName: DECANE / type: ligand / ID: 17 / Number of copies: 5 / Formula: D10
Molecular weightTheoretical: 142.282 Da
Chemical component information

ChemComp-D10:
DECANE

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Macromolecule #18: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 18 / Number of copies: 5 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID

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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
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number grids imaged: 1 / Number real images: 22699 / Average electron dose: 45.28 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 165000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 165000
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: 2569820
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: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.40) / Number images used: 62730
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.40)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.40)

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Atomic model buiding 1

Initial modelPDB ID:

7qnb


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: OTHER / Overall B value: 20 / Target criteria: FSC at 0.5
Output model

PDB-9fax:
CryoEM structure of human full-length beta3gamma2 GABA(A) receptor in complex with Megabody25, doubly occupied GARLH4 and Neuroligin2 TMD, in a closed state

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