SMTL ID : 9fat.1

CryoEM structure of human full-length alpha1beta3gamma2 GABA(A)R in complex with GARLH4, the TMD of Neuroligin2, Megabody38 and pregnenolone sulfate

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-(1-6)-[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: K.106 Chain C: S.76, N.77, V.79, G.80, K.81, K.94, W.99, P.103 Chain D: N.19, S.83, N.102, K.108 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.5 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:K.106, B:K.106, C:K.94, B:K.106

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.2: 9 residues within 4Å: Chain B: N.143, R.186, V.188, S.189, R.190, N.191, S.203, S.205, R.207 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.191 Hydrophobic interactions: B:V.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: 4 residues within 4Å: Chain B: P.72, L.73, N.74, H.113 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.7: 3 residues within 4Å: Chain E: L.73, N.74, H.113 No protein-ligand interaction detected (PLIP)

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: 7 residues within 4Å: Chain C: W.159, K.160, R.161, S.163, V.164, L.182, 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: 8 residues within 4Å: Chain A: L.80 Chain D: L.80, N.102, M.105 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, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.1 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain E Hydrophobic interactions: D:L.80 Hydrogen bonds: E:D.83

1 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.6: 8 residues within 4Å: Chain E: N.143, R.186, V.188, S.189, R.190, N.191, S.205, R.207 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:R.186, E:R.186, E:R.190

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: 11 residues within 4Å: Chain A: R.240, F.301, K.303, R.304, K.317, N.378, S.379, S.381, K.382, I.383, L.386 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:F.301, A:I.383, A:L.386 Hydrogen bonds: A:R.240, A:R.240, A:K.303, A:S.379, 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 PIO.21: 13 residues within 4Å: Chain D: R.240, T.297, F.301, K.303, R.304, K.317, N.378, S.379, S.381, K.382, I.383, L.386 Ligands: HEX.22 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:T.297, D:F.301, D:I.383, 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

3 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: G.215, V.218, I.219, I.226, M.227, F.395, N.399, W.403 Chain B: N.259, P.270, M.280, F.283 Ligands: D10.10 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:V.218, A:I.219, A:I.226, A:F.395, A:W.403, B:F.283 Hydrogen bonds: B:P.270 PGW.15: 18 residues within 4Å: Chain B: N.211, I.212, G.213, I.216, L.217, M.221, P.222, L.225 Chain C: S.256, S.267, L.274, S.277 Chain H: F.68, T.69, D.70, F.71, S.72 Ligands: CLR.17 14 PLIP interactions: 5 interactions with chain H, 7 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: H:F.68, H:F.71, B:I.216, B:L.217, B:M.221, B:P.222, B:L.225, C:L.274 Hydrogen bonds: H:D.70, H:F.71, H:S.72, B:I.212, B:G.213, C:S.267 PGW.24: 8 residues within 4Å: Chain H: R.7, V.11, A.14, I.15, I.18, F.103, F.104, Y.112 8 PLIP interactions: 8 interactions with chain H Hydrophobic interactions: H:A.14, H:I.15, H:I.18, H:F.103, H:F.104, H:F.104 Hydrogen bonds: H:Y.112 Salt bridges: H:R.7

3 x D10: DECANE(Non-functional Binders)(Non-covalent)

D10.10: 1 residues within 4Å: Ligands: PGW.9 No protein-ligand interaction detected (PLIP) D10.13: 3 residues within 4Å: Chain B: S.430, L.434 Ligands: R16.12 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.434, B:L.434 D10.18: 7 residues within 4Å: Chain C: L.392, L.395, V.396, V.399 Chain H: A.21, I.22, L.94 6 PLIP interactions: 3 interactions with chain H, 3 interactions with chain C Hydrophobic interactions: H:A.21, H:I.22, H:L.94, C:L.392, C:V.396, C:V.399

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

CL.11: 3 residues within 4Å: Chain A: V.44, N.180, Q.181 Ligand excluded by PLIP CL.25: 5 residues within 4Å: Chain H: F.49, S.67, F.68, T.69 Ligands: CLR.17 Ligand excluded by PLIP

1 x R16: HEXADECANE(Non-covalent)

R16.12: 5 residues within 4Å: Chain B: I.216, S.430, N.433, V.441 Ligands: D10.13 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.216, B:V.441

3 x HEX: HEXANE(Non-covalent)

HEX.14: 2 residues within 4Å: Chain B: E.292, F.295 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:E.292, B:F.295 HEX.22: 2 residues within 4Å: Chain D: E.294 Ligands: PIO.21 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:E.294 HEX.23: 1 residues within 4Å: Chain E: F.295 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:F.295

1 x PLM: PALMITIC ACID(Non-covalent)

PLM.16: 8 residues within 4Å: Chain C: C.361, H.372, R.374, Y.381, F.385 Chain H: L.102, C.106, T.110 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain H Hydrophobic interactions: C:Y.381, C:Y.381, C:F.385, C:F.385, H:L.102 Salt bridges: C:H.372, C:R.374

1 x CLR: CHOLESTEROL(Non-covalent)

CLR.17: 14 residues within 4Å: Chain C: L.274, F.393, V.396, S.400, Y.401 Chain H: I.29, F.68, T.69, L.87, L.94, G.95, T.98 Ligands: PGW.15, CL.25 10 PLIP interactions: 4 interactions with chain H, 6 interactions with chain C Hydrophobic interactions: H:I.29, H:F.68, H:T.69, H:L.87, C:L.274, C:F.393, C:F.393, C:V.396, C:V.396, C:Y.401

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

PX2.19: 7 residues within 4Å: Chain C: W.228, W.232, S.380, R.383, I.384 Chain D: Y.300 Chain H: F.105 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:W.228, C:W.232, C:I.384 Salt bridges: C:R.383 Hydrogen bonds: D:Y.300

1 x A8W: Pregnenolone sulfate(Non-covalent)

A8W.20: 14 residues within 4Å: Chain A: P.244, V.248 Chain B: A.242, A.246 Chain C: P.239, S.243, T.247, L.250 Chain D: P.244, V.248, L.255 Chain E: A.242, A.246, L.253 6 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 1 interactions with chain D, 1 interactions with chain C, 2 interactions with chain E Hydrophobic interactions: A:V.248, B:A.246, D:L.255, C:L.250, E:A.246, E:L.253

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, Megabody38 and pregnenolone sulfate. 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
Megabody38: F
Neuroligin-2: G
LHFPL tetraspan subfamily member 4 protein: H

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

B
B

E
E

C
C

F
G

G
H

H
L

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

Megabody38

Neuroligin-2

LHFPL tetraspan subfamily member 4 protein

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