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- EMDB-50276: CryoEM structure of gamma2 subunit of GABA(A)R in complex with GA... -

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Entry
Database: EMDB / ID: EMD-50276
TitleCryoEM structure of gamma2 subunit of GABA(A)R in complex with GARLH4, the TMD of Neuroligin2 from desensitised state obtained by focused refinement
Map dataPostprocessed map
Sample
  • Complex: CryoEM structure of gamma2 subunit of GABA(A)R in complex with GARLH4, the TMD of Neuroligin2 from desensitised state obtained by focused refinement
    • 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
  • Ligand: PALMITIC ACID
  • Ligand: CHOLESTEROL
  • Ligand: DECANE
  • Ligand: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate
  • Ligand: CHLORIDE ION
KeywordsGABA / Neurotransmission / Ternary complex / Inhibitory postsynapse / 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 / postsynaptic specialization / thigmotaxis / ribbon synapse / neuron cell-cell adhesion / insulin metabolic process / regulation of respiratory gaseous exchange by nervous system process / neurexin family protein binding / benzodiazepine receptor activity / inhibitory synapse / presynapse assembly / GABA receptor binding / protein localization to synapse / dopaminergic synapse / glycinergic synapse / regulation of AMPA receptor activity / positive regulation of inhibitory postsynaptic potential / cellular response to histamine / GABA receptor activation / GABA-A receptor activity / GABA-gated chloride ion channel activity / GABA-A receptor complex / inhibitory synapse assembly / positive regulation of synapse assembly / protein localization to cell surface / Neurexins and neuroligins / positive regulation of dendritic spine development / neurotransmitter receptor localization to postsynaptic specialization membrane / positive regulation of protein localization to synapse / postsynaptic specialization membrane / synaptic transmission, GABAergic / gamma-aminobutyric acid signaling pathway / chloride channel activity / social behavior / adult behavior / locomotory exploration behavior / Signaling by ERBB4 / neuromuscular process controlling balance / excitatory synapse / positive regulation of excitatory postsynaptic potential / regulation of presynapse assembly / chloride channel complex / synapse assembly / cell adhesion molecule binding / sensory perception of pain / dendrite membrane / cytoplasmic vesicle membrane / positive regulation of synaptic transmission, glutamatergic / chloride transmembrane transport / dendritic shaft / post-embryonic development / positive regulation of synaptic transmission, GABAergic / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / GABA-ergic synapse / sensory perception of sound / synapse organization / modulation of chemical synaptic transmission / positive regulation of insulin secretion / cell-cell adhesion / presynaptic membrane / dendritic spine / postsynaptic membrane / postsynapse / axon / positive regulation of cell population proliferation / synapse / dendrite / cell surface / 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 / Carboxylesterase type B, conserved site / Carboxylesterases type-B signature 2. / Carboxylesterase, type B / Carboxylesterase family ...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 / 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 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 / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Gamma-aminobutyric acid receptor subunit gamma-2 / LHFPL tetraspan subfamily member 4 protein / Neuroligin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
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)MC_EX_MR/T046279/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/L009609/1 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 gamma2 subunit of GABA(A)R in complex with GARLH4, the TMD of Neuroligin2 from desensitised state obtained by focused refinement
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

Supplemental images

emd_50276.png

Downloads & links

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Map

FileDownload / File: emd_50276.map.gz / Format: CCP4 / Size: 98.9 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.)
0.79 Å/pix.
x 296 pix.
= 234.719 Å		0.79 Å/pix.
x 296 pix.
= 234.719 Å		0.79 Å/pix.
x 296 pix.
= 234.719 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.79297 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.006
Minimum - Maximum-0.024278542 - 0.0544564
Average (Standard dev.)0.000040736537 (±0.0008279628)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions296296296
Spacing296296296
CellA=B=C: 234.71912 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_50276_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened map after focused refinement

Fileemd_50276_additional_1.map
AnnotationUnsharpened map after focused refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Input map used for the focused refinement

Fileemd_50276_additional_2.map
AnnotationInput map used for the focused refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: One of the halfmaps

Fileemd_50276_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_50276_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 gamma2 subunit of GABA(A)R in complex with GA...

EntireName: CryoEM structure of gamma2 subunit of GABA(A)R in complex with GARLH4, the TMD of Neuroligin2 from desensitised state obtained by focused refinement
Components
  • Complex: CryoEM structure of gamma2 subunit of GABA(A)R in complex with GARLH4, the TMD of Neuroligin2 from desensitised state obtained by focused refinement
    • 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
  • Ligand: PALMITIC ACID
  • Ligand: CHOLESTEROL
  • Ligand: DECANE
  • Ligand: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate
  • Ligand: CHLORIDE ION

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Supramolecule #1: CryoEM structure of gamma2 subunit of GABA(A)R in complex with GA...

SupramoleculeName: CryoEM structure of gamma2 subunit of GABA(A)R in complex with GARLH4, the TMD of Neuroligin2 from desensitised state obtained by focused refinement
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 300 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: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.923649 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
CLDGKDCASF F(P1L)(P1L)FED(P1L)RTG AWRHGRIHIR IAKMDSYARI FFPTAFCLFN LVYWVSYLYL G

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: 1 / 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: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 21.366189 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: YHEHYMRNSR AIGVLWAIFT ICFAIINVVV FIQPYWVGDS VSTPKPGYFG LFHYCVGSGL AGRELTCRGS FTDFSTIPSS AFKAAAFFV LLSMVLILGC ITCFSLFFFC NTATVYKICA WMQLLAALCL VLGCMIFPDG WDAETIRDMC GAKTGKYSLG D CSVRWAYI ...String:
YHEHYMRNSR AIGVLWAIFT ICFAIINVVV FIQPYWVGDS VSTPKPGYFG LFHYCVGSGL AGRELTCRGS FTDFSTIPSS AFKAAAFFV LLSMVLILGC ITCFSLFFFC NTATVYKICA WMQLLAALCL VLGCMIFPDG WDAETIRDMC GAKTGKYSLG D CSVRWAYI LAIIGILNAL ILSFLAFVLG NRQTD

UniProtKB: LHFPL tetraspan subfamily member 4 protein

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Macromolecule #4: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 4 / Number of copies: 1 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID

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Macromolecule #5: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 5 / Number of copies: 1 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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Macromolecule #6: DECANE

MacromoleculeName: DECANE / type: ligand / ID: 6 / Number of copies: 1 / Formula: D10
Molecular weightTheoretical: 142.282 Da
Chemical component information

ChemComp-D10:
DECANE

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Macromolecule #7: (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: 7 / Number of copies: 1 / Formula: PGW
Molecular weightTheoretical: 749.007 Da

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Macromolecule #8: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 8 / Number of copies: 1 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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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 / 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: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 22046 / Average electron dose: 46.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 130000 / 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 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: 2151332
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: RELION (ver. 3.1) / Number images used: 106412
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationSoftware - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6huo


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: OTHER / Overall B value: 10 / Target criteria: FSC at 0.5
Output model

PDB-9fan:
CryoEM structure of gamma2 subunit of GABA(A)R in complex with GARLH4, the TMD of Neuroligin2 from desensitised state obtained by focused refinement

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