SMTL ID : 9fan.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

1 x PLM: PALMITIC ACID(Non-covalent)

PLM.1: 7 residues within 4Å: Chain A: C.17, R.30, M.34, Y.37 Chain C: L.105, C.109, T.113 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:R.30, A:Y.37, C:L.105, C:T.113 Salt bridges: A:R.30 Hydrogen bonds: C:T.113

1 x CLR: CHOLESTEROL(Non-covalent)

CLR.2: 14 residues within 4Å: Chain A: C.17, F.49, V.52, S.56, Y.57 Chain C: I.32, F.52, F.71, M.93, V.94, L.97, G.98, T.101 Ligands: CL.5 8 PLIP interactions: 3 interactions with chain C, 5 interactions with chain A Hydrophobic interactions: C:I.32, C:F.71, C:V.94, A:F.49, A:F.49, A:V.52, A:V.52, A:Y.57

1 x D10: DECANE(Non-covalent)

D10.3: 5 residues within 4Å: Chain A: L.48, L.51, V.55 Chain C: I.25, L.97 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:L.48, A:L.51, A:V.55, C:L.97

1 x PGW: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate(Non-covalent)

PGW.4: 13 residues within 4Å: Chain A: T.44 Chain C: R.10, A.17, I.18, I.21, I.100, F.103, F.106, F.107, F.108, C.109, T.111, Y.115 13 PLIP interactions: 12 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:I.18, C:I.21, C:I.100, C:F.103, C:F.103, C:F.106, C:F.106, C:F.107, C:F.107, A:T.44 Hydrogen bonds: C:F.107 Salt bridges: C:R.10, C:R.10

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 4 residues within 4Å: Chain C: S.70, F.71, T.72 Ligands: CLR.2 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kasaragod, V.B. et al., CryoEM structure of gamma2 subunit of GABA(A)R in complex with GARLH4, the TMD of Neuroligin2 from desensitised state obtained by focused refinement. To Be Published

Release Date

2025-07-02

Peptides

Isoform 2 of Gamma-aminobutyric acid receptor subunit gamma-2: A
Neuroligin-2: B
LHFPL tetraspan subfamily member 4 protein: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
H

C
L

Membrane

We predict this structure to be a membrane protein.
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Isoform 2 of Gamma-aminobutyric acid receptor subunit gamma-2

Neuroligin-2

LHFPL tetraspan subfamily member 4 protein

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