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- PDB-9fan: CryoEM structure of gamma2 subunit of GABA(A)R in complex with GA... -

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Basic information

Entry
Database: PDB / ID: 9fan
TitleCryoEM structure of gamma2 subunit of GABA(A)R in complex with GARLH4, the TMD of Neuroligin2 from desensitised state obtained by focused refinement
Components
  • Isoform 2 of Gamma-aminobutyric acid receptor subunit gamma-2
  • LHFPL tetraspan subfamily member 4 protein
  • Neuroligin-2
KeywordsMEMBRANE PROTEIN / GABA / Neurotransmission / Ternary complex / Inhibitory postsynapse
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
CHOLESTEROL / DECANE / Chem-PGW / PALMITIC ACID / Gamma-aminobutyric acid receptor subunit gamma-2 / LHFPL tetraspan subfamily member 4 protein / Neuroligin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsKasaragod, V.B. / Aricescu, A.R.
Funding support United Kingdom, European Union, United States, 7items
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, V.B. / Aricescu, A.R.
History
DepositionMay 10, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: Additional map / Part number: 2 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jul 2, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Isoform 2 of Gamma-aminobutyric acid receptor subunit gamma-2
H: Neuroligin-2
L: LHFPL tetraspan subfamily member 4 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4748
Polymers32,9043
Non-polymers1,5705
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 2 types, 2 molecules CL

#1: Protein Isoform 2 of Gamma-aminobutyric acid receptor subunit gamma-2 / GABA(A) receptor subunit gamma-2 / GABAAR subunit gamma-2


Mass: 7923.649 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GABRG2 / Plasmid: pHR-TetO2 / Cell (production host): epithelial-like / Cell line (production host): HEK293S-TetR / Organ (production host): kidney / Production host: Homo sapiens (human) / Tissue (production host): kidney; embryo / References: UniProt: P18507
#3: Protein LHFPL tetraspan subfamily member 4 protein / GABAA receptor regulatory Lhfpl4 / Lipoma HMGIC fusion partner-like 4 protein


Mass: 21366.189 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LHFPL4, GARLH4 / Plasmid: pHR-TetO2 / Cell (production host): epithelial-like / Cell line (production host): HEK293S-TetR / Organ (production host): kidney / Production host: Homo sapiens (human) / Tissue (production host): kidney; embryo / References: UniProt: Q7Z7J7

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Protein/peptide , 1 types, 1 molecules H

#2: Protein/peptide Neuroligin-2


Mass: 3614.107 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NLGN2, KIAA1366 / Plasmid: pHR-TetO2 / Cell (production host): epithelial-like / Cell line (production host): HEK293S-TetR / Organ (production host): kidney / Production host: Homo sapiens (human) / Tissue (production host): kidney; embryo / References: UniProt: Q8NFZ4

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Non-polymers , 5 types, 5 molecules

#4: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#5: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H46O / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-D10 / DECANE


Mass: 142.282 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22
#7: Chemical ChemComp-PGW / (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate / 1-Palmitoyl-2-Oleoyl-sn-Glycero-3-[Phospho-(1-glycerol)] / PHOSPHATIDYLGLYCEROL


Mass: 749.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H77O10P / Comment: phospholipid*YM
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: 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 / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightValue: 0.3 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Strain: HEK293S
Buffer solutionpH: 7.4 / Details: 15 mM Hepes pH 7.4, 150 mM NaCl
Buffer component
IDConc.NameFormulaBuffer-ID
115 mM4-(2-hydroxyethyl)-1-piperazineethanesulfonic acidHEPES1
2150 mMSodium chlorideNaCl1
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Current: 30 mA / Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 287 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Calibrated magnification: 130000 X / Nominal defocus max: 2100 nm / Nominal defocus min: 700 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 46.6 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 22046
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1Warp1.0.9particle selection
2EPUimage acquisition
4CTFFIND4.1CTF correction
7PHENIXmodel fitting
9PHENIX19.2model refinement
10cryoSPARCinitial Euler assignment
11RELION3.1final Euler assignment
12RELION3.1classification
13RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2151332
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 106412 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 10 / Protocol: OTHER / Space: REAL / Target criteria: FSC at 0.5
Atomic model buildingPDB-ID: 6HUO

6huo


Accession code: 6HUO / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0042409
ELECTRON MICROSCOPYf_angle_d0.6673244
ELECTRON MICROSCOPYf_dihedral_angle_d12.623439
ELECTRON MICROSCOPYf_chiral_restr0.039356
ELECTRON MICROSCOPYf_plane_restr0.003380

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