SMTL ID : 9faw.1

CryoEM structure of human full-length beta3gamma2 GABA(A) receptor in complex with GARLH4, the TMD of Neuroligin2, HEPES and Megabody25, in a desensitised state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-1-1-1-3-mer

Ligands

4 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 4 residues within 4Å: Chain A: P.74, L.75, N.76, H.115 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 4 residues within 4Å: Chain B: P.74, L.75, N.76, H.115 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 4 residues within 4Å: Chain C: P.74, L.75, N.76, H.115 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.7: 3 residues within 4Å: Chain D: P.74, N.76, H.115 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN-MAN.2: 10 residues within 4Å: Chain A: N.145, R.188, V.190, S.191, R.192, N.193, S.207, R.209 Chain J: N.417, D.500 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain J Hydrogen bonds: A:R.188, A:R.192, J:Y.418, J:Y.418

2 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN.4: 9 residues within 4Å: Chain B: N.145, R.188, S.191, R.192, S.207, R.209 Chain I: N.417, Y.418, D.500 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:D.500, I:D.500 NAG-NAG-BMA-MAN-MAN-MAN.6: 12 residues within 4Å: Chain C: N.145, E.186, R.188, V.190, S.191, R.192, S.207, R.209 Chain H: N.417, Y.418, D.500, W.502 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain H Hydrogen bonds: C:R.192, C:R.188, H:D.500

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.8: 6 residues within 4Å: Chain D: N.145, R.188, S.191, R.192, S.207, R.209 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.188

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.9: 3 residues within 4Å: Chain E: W.163, R.165, N.188 No protein-ligand interaction detected (PLIP)

1 x HEX: HEXANE(Non-covalent)

HEX.10: 2 residues within 4Å: Chain A: G.283, V.286 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.286

3 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.11: 12 residues within 4Å: Chain A: Y.93, E.151, S.152, Y.153, F.196, A.197, T.198, Y.201 Chain C: N.37, D.39, Y.58, Q.60 6 PLIP interactions: 2 interactions with chain C, 4 interactions with chain A Salt bridges: C:D.39, A:E.151 pi-Cation interactions: C:Y.58, A:Y.201 Hydrogen bonds: A:S.152, A:T.198 EPE.13: 13 residues within 4Å: Chain B: Y.93, E.151, S.152, Y.153, F.196, A.197, T.198, Y.201 Chain D: D.39, Y.58, Q.60, M.111, T.172 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:E.151, B:A.197, D:Q.60, D:T.172 pi-Cation interactions: B:Y.153, B:F.196 EPE.15: 12 residues within 4Å: Chain B: D.39, Y.58, Q.60, T.172 Chain C: Y.93, E.151, S.152, Y.153, F.196, A.197, T.198, Y.201 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:Y.93, C:S.152, C:A.197, B:Q.60, B:T.172 Salt bridges: B:D.39

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.12: 18 residues within 4Å: Chain A: N.213, I.214, G.215, L.219, M.223, L.227 Chain E: S.260, S.271, V.273, L.278, S.281, F.284 Chain G: F.65, T.66, D.67, F.68, S.69 Ligands: CLR.17 7 PLIP interactions: 2 interactions with chain G, 4 interactions with chain E, 1 interactions with chain A Hydrophobic interactions: G:F.68, G:F.68, E:V.273, E:L.278, E:F.284, A:L.227 Hydrogen bonds: E:S.271

2 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.14: 5 residues within 4Å: Chain B: D.1, N.4, S.6, F.7, E.10 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.10 NAG.16: 4 residues within 4Å: Chain C: N.4, S.6, F.7, E.10 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:F.7, C:E.10

1 x CLR: CHOLESTEROL(Non-covalent)

CLR.17: 17 residues within 4Å: Chain E: L.278, A.393, F.397, V.400, S.404, Y.405 Chain G: F.25, I.26, F.46, S.64, F.65, T.66, L.84, M.87, V.88, L.91 Ligands: PGW.12 11 PLIP interactions: 4 interactions with chain E, 7 interactions with chain G Hydrophobic interactions: E:L.278, E:F.397, E:V.400, E:Y.405, G:F.25, G:I.26, G:F.65, G:F.65, G:L.84, G:V.88 Hydrogen bonds: G:F.65

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kasaragod, V.B. et al., CryoEM structure of human full-length beta3gamma2 GABA(A) receptor in complex with GARLH4, the TMD of Neuroligin2, HEPES and Megabody25, in a desensitised state. To Be Published

Release Date

2025-07-02

Peptides

Gamma-aminobutyric acid receptor subunit beta-3: ABCD
Isoform 2 of Gamma-aminobutyric acid receptor subunit gamma-2: E
Neuroligin-2: F
LHFPL tetraspan subfamily member 4 protein: G
Megabody25: HIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
E

C
A

D
D

E
C

F
H

G
L

H
K

I
O

J
F

Membrane

We predict this structure to be a membrane protein.
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Gamma-aminobutyric acid receptor subunit beta-3

Isoform 2 of Gamma-aminobutyric acid receptor subunit gamma-2

Neuroligin-2

LHFPL tetraspan subfamily member 4 protein

Megabody25

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