SMTL ID : 9faj.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 (StateD1)

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: 16 residues within 4Å: Chain A: N.102, T.104 Chain B: V.100, K.106 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.5 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:A.95

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: 3 residues within 4Å: Chain B: P.72, 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 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.186 NAG-NAG-BMA-MAN-MAN-MAN.6: 8 residues within 4Å: Chain E: N.143, E.184, R.186, S.189, R.190, S.203, S.205, R.207 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:R.186, 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: 6 residues within 4Å: Chain C: W.159, K.160, S.163, L.182, R.183, N.184 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-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.5: 7 residues within 4Å: Chain B: D.83 Chain D: N.102, M.105, P.106 Chain E: D.83 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.1, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.1 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:D.83, E:D.83

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.8: 15 residues within 4Å: Chain A: R.240, E.294, 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: D10.11 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:E.294, A:T.297, A:L.386, A:L.386 Hydrogen bonds: A:R.240, A:R.240, A:N.378, A:S.379, 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.34: 15 residues within 4Å: Chain D: R.240, I.293, F.301, K.303, R.304, K.317, F.377, N.378, S.379, S.381, K.382, I.383, L.386 Ligands: HEX.35, HEX.37 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:I.293, D:L.386 Hydrogen bonds: D:R.240, D:S.379, 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.9: 13 residues within 4Å: Chain A: K.213, I.214, G.215, L.223, I.226, I.230, P.392, F.395, N.399, W.403, L.407 Chain B: P.270 Ligands: PX2.17 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.226, A:I.230, A:P.392, A:F.395, A:N.399, A:W.403, A:W.403 Hydrogen bonds: A:G.215 PGW.36: 17 residues within 4Å: Chain D: K.213, I.214, G.215, V.218, L.223, P.224, I.226, P.392, F.395, N.399, W.403 Chain E: M.280, F.283, V.284 Ligands: D10.39, PX2.42, R16.48 13 PLIP interactions: 11 interactions with chain D, 2 interactions with chain E Hydrophobic interactions: D:I.214, D:V.218, D:L.223, D:P.224, D:I.226, D:P.392, D:N.399, D:W.403, D:W.403, E:F.283, E:V.284 Hydrogen bonds: D:I.214, D:G.215 PGW.45: 5 residues within 4Å: Chain A: A.272 Chain E: N.211, I.212, G.213 Ligands: R16.43 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:I.212, E:G.213 PGW.52: 21 residues within 4Å: Chain B: N.211, I.212, G.213, I.216, L.217, L.225 Chain C: S.256, S.267, Y.268, V.269, L.274, S.277, F.280, I.281 Chain G: F.71, T.72, D.73, F.74, S.75 Ligands: D10.24, CLR.32 13 PLIP interactions: 3 interactions with chain C, 5 interactions with chain B, 5 interactions with chain G Hydrophobic interactions: C:L.274, C:F.280, B:I.216, B:L.217, B:L.217, G:F.74 Hydrogen bonds: C:S.267, B:I.212, B:G.213, G:D.73, G:D.73, G:F.74, G:S.75 PGW.54: 13 residues within 4Å: Chain C: T.388, L.395 Chain G: R.10, A.17, I.18, I.21, I.100, F.103, F.106, F.107, F.108, Y.115 Ligands: D10.53 12 PLIP interactions: 10 interactions with chain G, 2 interactions with chain C Hydrophobic interactions: G:A.17, G:I.21, G:F.103, G:F.106, G:F.106, G:F.107, G:F.107, G:F.107, C:T.388, C:L.395 Hydrogen bonds: G:F.107 Salt bridges: G:R.10

12 x D10: DECANE(Non-covalent)

D10.10: 5 residues within 4Å: Chain A: A.282, Y.285, A.286, F.289 Chain E: L.225 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain E Hydrophobic interactions: A:Y.285, A:A.286, A:F.289, E:L.225 D10.11: 4 residues within 4Å: Chain A: I.293 Ligands: PIO.8, D10.15, PLM.47 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.293 D10.12: 3 residues within 4Å: Chain A: L.400, W.403, L.407 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.400, A:W.403, A:L.407 D10.15: 4 residues within 4Å: Chain A: Y.300 Ligands: D10.11, PLM.47, HEX.50 No protein-ligand interaction detected (PLIP) D10.19: 4 residues within 4Å: Chain B: S.430, L.434, W.437 Ligands: R16.18 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.434, B:W.437 D10.24: 3 residues within 4Å: Chain B: I.216 Ligands: R16.18, PGW.52 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.216 D10.27: 2 residues within 4Å: Chain C: F.296, H.372 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.296 D10.38: 6 residues within 4Å: Chain C: I.218, L.222 Chain D: A.282, A.286, F.289 Ligands: PX2.40 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:I.218, D:A.286, D:F.289 D10.39: 5 residues within 4Å: Chain D: G.396, L.400, L.407 Ligands: PGW.36, PX2.42 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:L.407 D10.44: 2 residues within 4Å: Chain E: W.437 Ligands: R16.43 No protein-ligand interaction detected (PLIP) D10.49: 6 residues within 4Å: Chain E: M.277, F.432, V.435, Y.439, Y.440 Ligands: R16.48 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:F.432, E:V.435, E:Y.439 D10.53: 7 residues within 4Å: Chain C: L.392, L.395, V.396, V.399 Chain G: I.25, L.97 Ligands: PGW.54 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain G Hydrophobic interactions: C:L.392, C:L.395, C:V.396, C:V.399, G:L.97

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

PX2.13: 11 residues within 4Å: Chain A: W.279, V.283, A.286, F.287, S.290, L.394, F.398, V.401, Y.402, T.405, Y.406 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:V.283, A:V.283, A:A.286, A:F.287, A:F.287, A:F.287, A:F.287, A:L.394, A:F.398, A:V.401, A:Y.402, A:T.405 PX2.17: 9 residues within 4Å: Chain A: V.234, W.237, R.388, P.392 Chain B: L.291, F.295, Y.298, R.303 Ligands: PGW.9 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:L.291, B:F.295, A:V.234, A:W.237, A:W.237, A:W.237 Salt bridges: B:R.303 PX2.26: 8 residues within 4Å: Chain C: S.380, R.383, I.384, P.387 Chain D: Y.300 Chain G: F.108 Ligands: PLM.29, PLM.31 5 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D, 1 interactions with chain G Hydrophobic interactions: C:R.383, C:I.384, C:P.387, G:F.108 Hydrogen bonds: D:Y.300 PX2.40: 13 residues within 4Å: Chain D: W.279, A.282, V.283, A.286, F.287, L.394, I.397, F.398, V.401, Y.402, Y.406 Ligands: HEX.35, D10.38 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:A.282, D:V.283, D:A.286, D:F.287, D:L.394, D:L.394, D:F.398, D:F.398, D:F.398, D:V.401, D:Y.402 PX2.42: 10 residues within 4Å: Chain D: V.234, W.237, R.388, P.392, G.396 Chain E: F.295, Y.298, R.303 Ligands: PGW.36, D10.39 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain E Hydrophobic interactions: D:V.234, D:W.237, D:W.237, D:W.237, D:P.392, E:Y.298 Hydrogen bonds: E:R.303

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

ABU.14: 10 residues within 4Å: Chain A: R.58, L.109, T.121 Chain B: Y.91, E.149, S.150, Y.151, F.194, T.196, Y.199 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.151, B:F.194, B:Y.199, A:L.109 Hydrogen bonds: B:Y.91, B:S.150, B:Y.151, B:T.196 Salt bridges: A:R.58 ABU.51: 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 7 PLIP interactions: 5 interactions with chain E, 2 interactions with chain D Hydrophobic interactions: E:Y.151, E:Y.199, D:L.109 Hydrogen bonds: E:Y.91, E:S.150, E:Y.199 Salt bridges: D:R.58

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

CL.16: 6 residues within 4Å: Chain A: P.43, V.44, L.179, N.180, Q.181, Y.182 Ligand excluded by PLIP CL.33: 5 residues within 4Å: Chain C: P.40, V.41, L.174, Y.175, Q.176 Ligand excluded by PLIP CL.41: 5 residues within 4Å: Chain D: V.44, L.179, N.180, Q.181, Y.182 Ligand excluded by PLIP CL.55: 5 residues within 4Å: Chain G: F.52, S.70, F.71, T.72 Ligands: CLR.32 Ligand excluded by PLIP

4 x R16: HEXADECANE(Non-covalent)

R16.18: 7 residues within 4Å: Chain B: I.224, W.231, S.430, W.437, V.441 Ligands: D10.19, D10.24 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:W.231, B:W.437, B:V.441 R16.22: 6 residues within 4Å: Chain B: M.277, L.431, F.432, V.435, Y.436, Y.439 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.431, B:F.432, B:F.432, B:V.435, B:Y.439, B:Y.439 R16.43: 7 residues within 4Å: Chain E: I.216, W.231, F.429, N.433, W.437 Ligands: D10.44, PGW.45 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:W.231, E:F.429, E:W.437 R16.48: 7 residues within 4Å: Chain E: V.272, M.277, G.281, V.284, F.432 Ligands: PGW.36, D10.49 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:V.272, E:V.284, E:F.432

7 x HEX: HEXANE(Non-covalent)

HEX.20: 1 residues within 4Å: Chain B: E.292 No protein-ligand interaction detected (PLIP) HEX.21: 4 residues within 4Å: Chain B: W.235, I.423, P.426 Ligands: PLM.30 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:W.235, B:I.423, B:P.426 HEX.23: 5 residues within 4Å: Chain B: M.277, M.280, G.281, V.284, F.285 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:M.280, B:V.284, B:F.285 HEX.35: 6 residues within 4Å: Chain D: F.287, S.290, F.391, L.394 Ligands: PIO.34, PX2.40 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:F.287, D:F.391, D:F.391 HEX.37: 3 residues within 4Å: Chain D: S.290, E.294 Ligands: PIO.34 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:E.294, D:E.294 HEX.46: 1 residues within 4Å: Chain E: E.292 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:E.292 HEX.50: 3 residues within 4Å: Chain E: I.423, P.426 Ligands: D10.15 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:I.423, E:P.426

5 x PLM: PALMITIC ACID(Non-covalent)

PLM.25: 7 residues within 4Å: Chain C: C.361, R.374, Y.381 Chain G: L.105, C.109, N.110, T.113 6 PLIP interactions: 4 interactions with chain G, 2 interactions with chain C Hydrophobic interactions: G:L.105, G:T.113, C:Y.381 Hydrogen bonds: G:N.110, G:T.113 Salt bridges: C:R.374 PLM.29: 6 residues within 4Å: Chain C: F.390, N.394, W.398, L.402 Ligands: PX2.26, OLC.28 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.390, C:W.398, C:W.398 PLM.30: 8 residues within 4Å: Chain B: W.231, V.232, W.235 Chain C: T.292, Y.295, F.296, R.300 Ligands: HEX.21 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:W.231, B:V.232, B:W.235, B:W.235, B:W.235, C:Y.295, C:Y.295, C:F.296 Salt bridges: C:R.300 PLM.31: 6 residues within 4Å: Chain C: W.228, V.229, W.232 Chain D: T.297, Y.300 Ligands: PX2.26 7 PLIP interactions: 2 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:Y.300, D:Y.300, C:W.228, C:V.229, C:W.232, C:W.232, C:W.232 PLM.47: 7 residues within 4Å: Chain A: I.293, T.297, Y.300, F.301 Chain E: W.235 Ligands: D10.11, D10.15 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain E Hydrophobic interactions: A:I.293, A:Y.300, E:W.235, E:W.235, E:W.235

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

OLC.28: 8 residues within 4Å: Chain C: R.208, M.209, G.210, I.214 Chain D: D.278, W.279, A.282 Ligands: PLM.29 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:I.214, D:W.279, D:A.282 Hydrogen bonds: C:M.209, C:G.210

1 x CLR: CHOLESTEROL(Non-covalent)

CLR.32: 16 residues within 4Å: Chain C: L.274, C.361, F.393, V.396, S.400, Y.401 Chain G: I.32, F.52, F.71, T.72, L.90, L.97, G.98, T.101 Ligands: PGW.52, CL.55 11 PLIP interactions: 5 interactions with chain G, 6 interactions with chain C Hydrophobic interactions: G:I.32, G:F.71, G:T.72, G:L.90, G:L.97, C:L.274, C:L.274, 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 (StateD1). 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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