SMTL ID : 9faq.1

CryoEM structure of human full-length alpha1beta3gamma2 GABA(A)R in complex with GARLH4, the TMD of Neuroligin2 and Megabody38 in a closed state (StateC2)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-1-1-1-1-mer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-MAN-MAN-MAN-MAN-MAN.1: 17 residues within 4Å: Chain A: N.100, T.102 Chain B: R.78 Chain C: S.74, N.75, G.78, K.79, D.94, W.97, P.101 Chain D: N.17, K.95, A.98, N.100, P.104, K.106 Ligands: NAG-NAG-BMA-MAN.4 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.94

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.2: 8 residues within 4Å: Chain B: N.141, R.184, V.186, S.187, R.188, N.189, S.203, R.205 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.184 NAG-NAG-BMA-MAN-MAN-MAN.5: 9 residues within 4Å: Chain E: N.141, E.182, R.184, V.186, S.187, R.188, N.189, S.203, R.205 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:R.184, E:R.184, E:R.188

2 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.3: 3 residues within 4Å: Chain B: P.70, N.72, H.111 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.6: 3 residues within 4Å: Chain E: P.70, N.72, H.111 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN: 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.4: 8 residues within 4Å: Chain D: N.100, T.102, M.103, P.104 Chain E: D.81 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.1, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.1, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.1 No protein-ligand interaction detected (PLIP)

2 x PIO: [(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate(Non-covalent)

PIO.7: 11 residues within 4Å: Chain A: R.238, T.295, F.299, K.301, R.302, N.376, S.377, S.379, K.380, I.381, L.384 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:T.295, A:I.381, A:L.384 Hydrogen bonds: A:R.238, A:R.238, A:S.377, A:S.377, A:K.380 Salt bridges: A:R.238, A:K.301, A:K.301, A:R.302, A:K.380, A:K.380 PIO.18: 16 residues within 4Å: Chain D: R.238, I.291, T.295, F.299, K.301, R.302, K.315, N.376, S.377, S.379, K.380, I.381, L.384 Ligands: PX2.17, HEX.19, HEX.21 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:I.291, D:L.384 Hydrogen bonds: D:R.238, D:S.377, D:S.377, D:K.380, D:I.381 Salt bridges: D:R.238, D:K.301, D:K.301, D:R.302, D:K.315, D:K.315, D:K.380, D:K.380

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

PGW.8: 10 residues within 4Å: Chain A: I.212, G.213, V.216, L.221, I.224, F.393, G.394, N.397, W.401 Chain B: V.282 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.212, A:V.216, A:L.221, A:L.221, A:I.224, A:F.393, A:W.401, B:V.282 Hydrogen bonds: A:I.212, A:G.213 PGW.10: 18 residues within 4Å: Chain B: N.209, I.210, G.211, I.214, M.219, P.220, L.223, W.435 Chain C: S.254, S.265, V.267, S.275, F.278, I.279 Chain G: T.72, D.73, F.74, S.75 16 PLIP interactions: 9 interactions with chain B, 3 interactions with chain G, 4 interactions with chain C Hydrophobic interactions: B:I.214, B:M.219, B:P.220, B:L.223, B:W.435, B:W.435, C:V.267, C:F.278, C:I.279 Hydrogen bonds: B:S.179, B:I.210, B:G.211, G:F.74, G:S.75, G:S.75, C:S.265 PGW.20: 13 residues within 4Å: Chain D: R.210, K.211, I.212, G.213, V.216, I.217, L.221, F.393, N.397, W.401 Chain E: M.275, V.282, L.286 12 PLIP interactions: 10 interactions with chain D, 2 interactions with chain E Hydrophobic interactions: D:V.216, D:I.217, D:L.221, D:F.393, D:N.397, D:W.401, D:W.401, E:V.282, E:L.286 Hydrogen bonds: D:R.210, D:I.212, D:G.213 PGW.22: 5 residues within 4Å: Chain D: W.277, V.399, Y.400, T.403, Y.404 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:W.277 Hydrogen bonds: D:T.403, D:Y.404 PGW.25: 12 residues within 4Å: Chain C: T.386, L.393 Chain G: R.10, A.17, I.18, I.21, I.100, F.103, F.106, F.107, F.108, Y.115 10 PLIP interactions: 8 interactions with chain G, 2 interactions with chain C Hydrophobic interactions: G:A.17, G:I.18, G:I.21, G:I.21, G:F.106, C:T.386, C:L.393 Hydrogen bonds: G:F.107 Salt bridges: G:R.10, G:R.10

2 x D10: DECANE(Non-covalent)

D10.9: 3 residues within 4Å: Chain B: S.428, L.432, W.435 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.432, B:W.435 D10.24: 5 residues within 4Å: Chain C: L.393, V.394, V.397 Chain G: I.25, L.97 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain G Hydrophobic interactions: C:L.393, C:V.394, C:V.397, G:L.97

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

NAG.11: 3 residues within 4Å: Chain C: W.157, S.161, N.182 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.161, C:S.161

5 x PLM: PALMITIC ACID(Non-covalent)

PLM.12: 7 residues within 4Å: Chain C: D.358, C.359, R.372, Y.379 Chain G: L.105, C.109, T.113 6 PLIP interactions: 2 interactions with chain G, 4 interactions with chain C Hydrophobic interactions: G:L.105, G:T.113, C:R.372, C:Y.379, C:Y.379 Salt bridges: C:R.372 PLM.14: 7 residues within 4Å: Chain C: M.207, T.211, T.219, F.388, N.392, W.396 Ligands: PX2.17 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:T.219, C:F.388, C:W.396, C:W.396 Hydrogen bonds: C:T.211 PLM.15: 5 residues within 4Å: Chain B: W.229, W.233 Chain C: T.290, Y.293, F.294 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:Y.293, C:Y.293, C:F.294, C:F.294, B:W.229, B:W.233 Hydrogen bonds: C:Y.293 PLM.16: 7 residues within 4Å: Chain C: W.226, V.227, W.230 Chain D: I.291, T.295, Y.298 Ligands: PX2.17 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:W.226, C:V.227, C:W.230, C:W.230, C:W.230, D:I.291, D:Y.298 PLM.23: 8 residues within 4Å: Chain A: I.291, A.294, T.295, Y.298, F.299 Chain E: W.229, V.230, W.233 10 PLIP interactions: 5 interactions with chain E, 5 interactions with chain A Hydrophobic interactions: E:W.229, E:V.230, E:W.233, E:W.233, E:W.233, A:I.291, A:T.295, A:Y.298, A:Y.298, A:F.299

1 x CLR: CHOLESTEROL(Non-covalent)

CLR.13: 14 residues within 4Å: Chain C: L.272, F.391, V.394, S.398, Y.399 Chain G: I.32, F.52, F.71, T.72, L.90, L.97, G.98, T.101 Ligands: CL.26 8 PLIP interactions: 4 interactions with chain C, 4 interactions with chain G Hydrophobic interactions: C:F.391, C:V.394, C:V.394, C:Y.399, G:I.32, G:F.71, G:T.72, G:L.90

1 x PX2: 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE(Non-covalent)

PX2.17: 9 residues within 4Å: Chain C: W.226, W.230, R.381, I.382 Chain D: Y.298 Chain G: F.108 Ligands: PLM.14, PLM.16, PIO.18 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:W.226, C:W.230, C:I.382 Salt bridges: C:R.381 Hydrogen bonds: D:Y.298

2 x HEX: HEXANE(Non-covalent)

HEX.19: 5 residues within 4Å: Chain D: F.285, S.288, F.389, L.392 Ligands: PIO.18 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:F.285, D:F.389 HEX.21: 3 residues within 4Å: Chain D: S.288, E.292 Ligands: PIO.18 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:E.292

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

CL.26: 3 residues within 4Å: Chain C: N.131 Chain G: S.70 Ligands: CLR.13 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kasaragod, V.B. et al., CryoEM structure of human full-length alpha1beta3gamma2 GABA(A)R in complex with GARLH4, the TMD of Neuroligin2 and Megabody38 in a closed state (StateC2). To Be Published

Release Date

2025-07-02

Peptides

Gamma-aminobutyric acid receptor subunit alpha-1: AD
Gamma-aminobutyric acid receptor subunit beta-3: BE
Isoform 2 of Gamma-aminobutyric acid receptor subunit gamma-2: C
Neuroligin-2: F
LHFPL tetraspan subfamily member 4 protein: G
Megabody38: H

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

B
B

E
E

C
C

F
H

G
L

H
G

Membrane

We predict this structure to be a membrane protein.
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Gamma-aminobutyric acid receptor subunit alpha-1

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

Megabody38

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