SMTL ID : 9fak.1

CryoEM structure of human full-length alpha1beta3gamma2 GABA(A) receptor in complex with GARLH4, the TMD of Neuroligin2, GABA and Megabody38 in a desensitised state (StateD2)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-1-1-1-2-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-(1-6)-[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-MAN-MAN-MAN-MAN-MAN.1: 15 residues within 4Å: Chain A: N.102, T.104 Chain B: V.100 Chain C: S.76, N.77, G.80, K.81, D.96, W.99 Chain D: N.19, S.83, N.102, P.106, K.108 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.5 No protein-ligand interaction detected (PLIP)

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.2: 2 residues within 4Å: Chain B: N.74, H.113 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.7: 4 residues within 4Å: Chain E: P.72, L.73, N.74, H.113 No protein-ligand interaction detected (PLIP)

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.3: 7 residues within 4Å: Chain B: N.143, R.186, V.188, S.189, R.190, S.205, R.207 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.186, B:R.186 NAG-NAG-BMA-MAN-MAN-MAN.6: 8 residues within 4Å: Chain E: N.143, R.186, V.188, S.189, R.190, S.203, S.205, R.207 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:R.186, E:S.203

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.4: 5 residues within 4Å: Chain C: W.159, K.160, R.161, S.163, N.184 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: 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.5: 9 residues within 4Å: Chain A: L.80, S.83 Chain B: D.83 Chain D: N.102, P.106 Chain E: D.83, Q.84 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.1, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.1 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:Q.84, E:D.83

6 x HEX: HEXANE(Non-covalent)

HEX.8: 6 residues within 4Å: Chain A: F.287, S.290, F.391, L.394 Ligands: PIO.9, PX2.13 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.287, A:F.391, A:F.391 HEX.19: 2 residues within 4Å: Chain B: E.292, W.420 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:E.292, B:W.420 HEX.20: 3 residues within 4Å: Chain B: R.422, I.423 Ligands: PLM.27 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.423 HEX.33: 2 residues within 4Å: Chain D: S.290 Ligands: PIO.29 No protein-ligand interaction detected (PLIP) HEX.43: 3 residues within 4Å: Chain E: L.288, L.291, E.292 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:L.291, E:E.292 HEX.45: 1 residues within 4Å: Chain E: W.235 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:W.235

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.9: 14 residues within 4Å: Chain A: R.240, T.297, F.301, K.303, R.304, K.317, N.378, S.379, S.381, K.382, I.383, L.386, S.387 Ligands: HEX.8 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:T.297, A:K.382 Hydrogen bonds: A:R.240, A:R.240, A:N.378, A:S.379, A:S.381, A:K.382, A:K.382, A:K.382 Salt bridges: A:R.240, A:K.303, A:K.303, A:R.304, A:K.317, A:K.317, A:K.382, A:K.382 PIO.29: 15 residues within 4Å: Chain D: R.240, I.293, T.297, F.301, K.303, R.304, K.317, N.378, S.379, S.381, K.382, I.383, L.386 Ligands: PX2.24, HEX.33 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:I.293, D:T.297, D:L.386 Hydrogen bonds: D:R.240, D:S.379, D:K.382 Salt bridges: D:R.240, D:K.303, D:K.303, D:R.304, D:K.317, D:K.317, D:K.382, D:K.382

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.10: 18 residues within 4Å: Chain A: R.212, K.213, I.214, G.215, L.223, I.226, M.227, F.395, N.399, W.403 Chain B: N.259, P.270, M.280, F.283, V.284 Ligands: PX2.11, D10.12, R16.22 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.223, A:I.226, A:F.395, B:F.283, B:V.284 Hydrogen bonds: A:R.212, A:I.214, A:G.215 PGW.30: 15 residues within 4Å: Chain D: K.213, I.214, G.215, V.218, I.219, L.223, P.224, I.226, N.399, W.403 Chain E: M.280, F.283, V.284 Ligands: PX2.31, D10.35 13 PLIP interactions: 11 interactions with chain D, 2 interactions with chain E Hydrophobic interactions: D:I.214, D:V.218, D:V.218, D:I.219, D:P.224, D:I.226, D:I.226, D:N.399, D:W.403, E:F.283, E:V.284 Hydrogen bonds: D:I.214, D:G.215 PGW.42: 7 residues within 4Å: Chain A: A.272 Chain E: N.211, I.212, G.213, I.216, L.217 Ligands: R16.39 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:I.216, E:L.217 Hydrogen bonds: E:I.212, E:G.213 PGW.47: 16 residues within 4Å: Chain B: N.211, I.212, G.213, L.217, M.221, L.225 Chain C: S.267, Y.268, V.269, S.277, I.281 Chain G: F.71, T.72, D.73, F.74 Ligands: CLR.48 9 PLIP interactions: 4 interactions with chain G, 2 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: G:F.71, G:F.74, C:V.269 Hydrogen bonds: G:D.73, G:F.74, B:I.212, B:G.213, C:S.267, C:S.267 PGW.50: 11 residues within 4Å: Chain C: T.388 Chain G: R.10, A.17, I.18, I.21, I.100, F.103, F.106, F.107, F.108, Y.115 12 PLIP interactions: 11 interactions with chain G, 1 interactions with chain C Hydrophobic interactions: G:A.17, G:I.21, G:I.21, G:I.100, G:F.103, G:F.106, G:F.107, G:F.107, C:T.388 Hydrogen bonds: G:F.107 Salt bridges: G:R.10, G:R.10

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

PX2.11: 8 residues within 4Å: Chain A: V.234, W.237, R.388, I.389, P.392 Chain B: F.295, Y.298 Ligands: PGW.10 9 PLIP interactions: 2 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:F.295, B:Y.298, A:V.234, A:W.237, A:W.237, A:W.237, A:I.389, A:P.392 Salt bridges: A:R.385 PX2.13: 12 residues within 4Å: Chain A: W.279, V.283, F.287, L.394, I.397, F.398, V.401, Y.402, T.405, Y.406, R.409 Ligands: HEX.8 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:W.279, A:V.283, A:F.287, A:L.394, A:L.394, A:I.397, A:F.398, A:F.398, A:V.401, A:V.401, A:V.401, A:Y.402 Hydrogen bonds: A:Y.406 Salt bridges: A:R.409 PX2.24: 9 residues within 4Å: Chain C: W.228, W.232, S.380, R.383, P.387 Chain D: Y.300 Chain G: F.108 Ligands: PIO.29, PLM.32 7 PLIP interactions: 5 interactions with chain C, 1 interactions with chain D, 1 interactions with chain G Hydrophobic interactions: C:W.228, C:W.232, C:W.232, C:P.387, G:F.108 Hydrogen bonds: C:R.383, D:Y.300 PX2.31: 6 residues within 4Å: Chain D: W.237, R.388, P.392 Chain E: L.291, Y.298 Ligands: PGW.30 6 PLIP interactions: 3 interactions with chain E, 3 interactions with chain D Hydrophobic interactions: E:L.291, E:Y.298, E:Y.298, D:W.237, D:W.237, D:W.237 PX2.36: 11 residues within 4Å: Chain D: W.279, V.283, F.287, S.290, F.391, L.394, I.397, F.398, V.401, Y.402, Y.406 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:V.283, D:V.283, D:F.287, D:F.287, D:F.391, D:L.394, D:L.394, D:L.394, D:I.397, D:F.398, D:V.401, D:Y.402

7 x D10: DECANE(Non-covalent)

D10.12: 4 residues within 4Å: Chain A: G.396, L.400, L.407 Ligands: PGW.10 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.400, A:L.407 D10.18: 4 residues within 4Å: Chain B: S.430, L.434, W.437, L.438 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.434, B:L.434, B:W.437 D10.34: 4 residues within 4Å: Chain C: I.218, L.222 Chain D: A.282, A.286 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:A.282, D:A.286, C:I.218, C:L.222 D10.35: 4 residues within 4Å: Chain D: G.396, L.400, L.407 Ligands: PGW.30 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:L.400, D:L.400, D:L.407 D10.38: 5 residues within 4Å: Chain A: A.282, Y.285, F.289 Chain E: M.221, L.225 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain A Hydrophobic interactions: E:L.225, A:Y.285, A:F.289 D10.40: 3 residues within 4Å: Chain E: L.434, W.437 Ligands: R16.39 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:L.434 D10.49: 6 residues within 4Å: Chain C: L.392, V.396, V.399 Chain G: A.24, I.25, L.97 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain G Hydrophobic interactions: C:L.392, C:V.396, C:V.399, G:A.24, G:L.97

8 x PLM: PALMITIC ACID(Non-covalent)

PLM.14: 6 residues within 4Å: Chain A: I.293, T.297, Y.300, F.301 Chain E: I.228, W.235 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain E Hydrophobic interactions: A:Y.300, A:Y.300, A:Y.300, A:F.301, E:I.228, E:W.235 PLM.21: 6 residues within 4Å: Chain B: T.428, F.432, V.435, Y.439, Y.440 Ligands: R16.22 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:T.428, B:F.432, B:V.435, B:Y.439, B:Y.439, B:Y.440 PLM.23: 8 residues within 4Å: Chain C: C.361, R.374, Y.381, F.385 Chain G: L.105, C.109, N.110, T.113 8 PLIP interactions: 4 interactions with chain C, 4 interactions with chain G Hydrophobic interactions: C:Y.381, C:Y.381, C:F.385, G:L.105, G:T.113 Salt bridges: C:R.374 Hydrogen bonds: G:N.110, G:T.113 PLM.26: 8 residues within 4Å: Chain C: M.209, T.213, T.221, V.225, C.391, N.394, W.398 Ligands: OLC.25 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:T.213, C:T.221, C:V.225 PLM.27: 8 residues within 4Å: Chain B: W.231, V.232, W.235 Chain C: T.292, Y.295, F.296, R.300 Ligands: HEX.20 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:W.231, B:V.232, B:W.235, B:W.235, B:W.235, C:F.296 Salt bridges: C:R.300 PLM.32: 7 residues within 4Å: Chain C: V.225, V.229, W.232 Chain D: T.297, Y.300, F.301 Ligands: PX2.24 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:V.225, C:V.229, C:W.232, C:W.232, D:T.297, D:Y.300, D:F.301 PLM.41: 8 residues within 4Å: Chain E: V.272, M.277, L.431, F.432, V.435, Y.439, Y.440 Ligands: PLM.44 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:L.431, E:F.432, E:Y.439, E:Y.440 PLM.44: 5 residues within 4Å: Chain E: V.272, M.277, G.281, V.284 Ligands: PLM.41 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:V.284

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

CL.15: 5 residues within 4Å: Chain A: V.44, L.179, N.180, Q.181, Y.182 Ligand excluded by PLIP CL.28: 7 residues within 4Å: Chain C: P.40, V.41, R.173, L.174, Y.175, Q.176, F.177 Ligand excluded by PLIP CL.37: 4 residues within 4Å: Chain D: P.43, V.44, N.180, Q.181 Ligand excluded by PLIP CL.51: 4 residues within 4Å: Chain G: F.52, S.70, F.71 Ligands: CLR.48 Ligand excluded by PLIP

2 x ABU: GAMMA-AMINO-BUTANOIC ACID(Non-covalent)

ABU.16: 11 residues within 4Å: Chain A: F.56, R.58, L.109, T.121 Chain B: Y.91, E.149, S.150, Y.151, F.194, T.196, Y.199 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:F.194, B:Y.199, A:L.109 Hydrogen bonds: B:Y.91, B:S.150, B:T.196, A:T.121 Salt bridges: A:R.58 ABU.46: 11 residues within 4Å: Chain D: F.56, R.58, L.109, T.121 Chain E: Y.91, E.149, S.150, Y.151, F.194, T.196, Y.199 10 PLIP interactions: 7 interactions with chain E, 3 interactions with chain D Hydrophobic interactions: E:Y.151, E:F.194, E:Y.199, D:F.56, D:L.109 Hydrogen bonds: E:Y.91, E:S.150, E:T.196, E:Y.199 Salt bridges: D:R.58

3 x R16: HEXADECANE(Non-covalent)

R16.17: 5 residues within 4Å: Chain B: F.429, S.430, N.433, W.437, V.441 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.429, B:W.437, B:W.437, B:W.437, B:V.441 R16.22: 6 residues within 4Å: Chain B: Y.271, V.272, M.277, G.281 Ligands: PGW.10, PLM.21 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.271, B:V.272 R16.39: 8 residues within 4Å: Chain E: I.212, I.216, W.231, F.429, N.433, W.437 Ligands: D10.40, PGW.42 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:I.212, E:W.231, E:F.429, E:W.437, E:W.437

1 x OLC: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)

OLC.25: 10 residues within 4Å: Chain C: R.207, R.208, M.209, G.210, I.214 Chain D: S.261, D.278, W.279, A.282 Ligands: PLM.26 6 PLIP interactions: 2 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:W.279, D:A.282, C:I.214 Hydrogen bonds: C:R.207, C:M.209, C:G.210

1 x CLR: CHOLESTEROL(Non-covalent)

CLR.48: 15 residues within 4Å: Chain C: L.274, C.361, F.393, V.396, Y.401 Chain G: I.32, F.52, F.71, T.72, L.90, L.97, G.98, T.101 Ligands: PGW.47, CL.51 9 PLIP interactions: 5 interactions with chain G, 4 interactions with chain C Hydrophobic interactions: G:I.32, G:F.71, G:T.72, G:L.90, G:T.101, C:F.393, C:V.396, C:V.396, C:Y.401

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kasaragod, V.B. et al., CryoEM structure of human full-length alpha1beta3gamma2 GABA(A) receptor in complex with GARLH4, the TMD of Neuroligin2, GABA and Megabody38 in a desensitised state (StateD2). 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: HI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

B
B

E
E

C
C

F
H

G
L

H
G

I
P

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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