SMTL ID : 9fas.1

CryoEM structure of human full-length alpha1beta3gamma2L GABA(A)R in complex with pregnenolone sulfate

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-1-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: 17 residues within 4Å: Chain A: N.102, T.104 Chain B: V.100, K.106 Chain C: S.76, N.77, V.79, G.80, K.81, A.95, D.96, W.99 Chain D: N.19, N.102, P.106, K.108 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.4 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Water bridges: B:V.100, B:H.101, B:G.102, B:G.102 Hydrogen bonds: C:D.96, B:K.106, B:K.106

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.6: 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: 8 residues within 4Å: Chain B: N.143, E.184, 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 Water bridges: B:S.203 NAG-NAG-BMA-MAN-MAN-MAN.5: 7 residues within 4Å: Chain E: N.143, R.186, V.188, S.189, R.190, S.205, R.207 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:R.186

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.4: 10 residues within 4Å: Chain A: L.80, S.83 Chain D: N.102, T.104, 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, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.1 No protein-ligand interaction detected (PLIP)

8 x HEX: HEXANE(Non-covalent)

HEX.7: 4 residues within 4Å: Chain A: F.287, S.290, F.391, L.394 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.287, A:F.287, A:F.391, A:F.391, A:L.394 HEX.20: 1 residues within 4Å: Chain B: E.292 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:E.292 HEX.22: 3 residues within 4Å: Chain B: M.277, M.280, G.281 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:M.280 HEX.30: 4 residues within 4Å: Chain B: M.221, L.225 Chain C: S.277, I.281 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:L.225, C:I.281 HEX.35: 4 residues within 4Å: Chain D: F.287, S.290, F.391, L.394 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:F.287, D:F.391, D:L.394 HEX.37: 3 residues within 4Å: Chain D: S.290, E.294 Ligands: PIO.34 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:E.294 HEX.47: 2 residues within 4Å: Chain E: E.292, F.295 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:E.292, E:F.295 HEX.50: 1 residues within 4Å: Chain E: I.423 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:I.423

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: 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: D10.11 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:K.382, A:I.383, A:I.383, A:L.386 Hydrogen bonds: A:R.240, A:R.240, A:N.378, A:S.379, A:S.381, 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: 14 residues within 4Å: Chain D: R.240, T.297, F.301, K.303, R.304, K.317, N.378, S.379, V.380, S.381, K.382, I.383, L.386 Ligands: HEX.37 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:T.297, D:L.386 Hydrogen bonds: D:R.240, D:R.240, D:S.379, D:V.380, 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: 12 residues within 4Å: Chain A: K.213, I.214, G.215, L.223, I.226, F.395, N.399, W.403 Chain B: P.270, M.280, F.283 Ligands: D10.12 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.223, A:I.226, A:I.226, A:F.395, B:F.283 Hydrogen bonds: A:I.214, A:G.215 PGW.13: 6 residues within 4Å: Chain A: W.279, F.398, V.401, T.405, Y.406, R.409 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.398, A:V.401 Hydrogen bonds: A:Y.406, A:R.409 Salt bridges: A:R.409 PGW.36: 15 residues within 4Å: Chain D: K.213, I.214, G.215, V.218, L.223, I.226, M.227, F.395, N.399, W.403 Chain E: N.259, P.270, F.283, V.284 Ligands: D10.39 11 PLIP interactions: 2 interactions with chain E, 9 interactions with chain D Hydrophobic interactions: E:F.283, E:V.284, D:V.218, D:L.223, D:I.226, D:F.395, D:N.399, D:W.403, D:W.403 Hydrogen bonds: D:I.214, D:G.215

17 x D10: DECANE(Non-covalent)

D10.10: 4 residues within 4Å: Chain A: S.261, A.282, Y.285 Chain E: L.225 Ligand excluded by PLIP D10.11: 2 residues within 4Å: Chain A: T.297 Ligands: PIO.8 Ligand excluded by PLIP D10.12: 3 residues within 4Å: Chain A: L.400, W.403 Ligands: PGW.9 Ligand excluded by PLIP D10.15: 3 residues within 4Å: Chain A: Y.300 Chain E: W.235 Ligands: PLM.14 Ligand excluded by PLIP D10.19: 5 residues within 4Å: Chain B: S.430, L.434, W.437, V.441 Ligands: R16.18 Ligand excluded by PLIP D10.23: 4 residues within 4Å: Chain B: N.211, I.212, G.213 Chain C: S.267 Ligand excluded by PLIP D10.24: 4 residues within 4Å: Chain B: I.228, W.235, I.423 Ligands: D10.25 Ligand excluded by PLIP D10.25: 4 residues within 4Å: Chain B: W.235 Chain C: Y.295, F.296 Ligands: D10.24 Ligand excluded by PLIP D10.27: 3 residues within 4Å: Chain C: W.232, S.388, I.392 Ligand excluded by PLIP D10.31: 2 residues within 4Å: Chain C: L.274, Y.409 Ligand excluded by PLIP D10.38: 2 residues within 4Å: Chain D: A.282, F.289 Ligand excluded by PLIP D10.39: 3 residues within 4Å: Chain D: L.400, L.407 Ligands: PGW.36 Ligand excluded by PLIP D10.40: 1 residues within 4Å: Chain D: W.237 Ligand excluded by PLIP D10.42: 4 residues within 4Å: Chain D: W.279, V.401, Y.402, Y.406 Ligand excluded by PLIP D10.43: 4 residues within 4Å: Chain D: V.234, W.237 Chain E: F.295, Y.298 Ligand excluded by PLIP D10.46: 1 residues within 4Å: Chain E: W.437 Ligand excluded by PLIP D10.49: 5 residues within 4Å: Chain E: M.277, F.432, V.435, Y.439, Y.440 Ligand excluded by PLIP

3 x PLM: PALMITIC ACID(Non-covalent)

PLM.14: 6 residues within 4Å: Chain A: I.293, T.297, Y.300 Chain E: V.232, W.235 Ligands: D10.15 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain E Hydrophobic interactions: A:Y.300, A:Y.300, E:V.232, E:W.235 PLM.26: 8 residues within 4Å: Chain C: M.209, T.221, W.228, F.398, C.399, N.402, W.406, L.410 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:W.228, C:F.398, C:W.406 PLM.32: 5 residues within 4Å: Chain C: W.228, W.232 Chain D: I.293, T.297, Y.300 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:W.228, C:W.232, C:W.232, C:W.232, D:I.293, D:Y.300

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

CL.16: 5 residues within 4Å: Chain A: V.44, L.179, N.180, Q.181, Y.182 Ligand excluded by PLIP CL.33: 3 residues within 4Å: Chain C: V.41, Y.175, Q.176 Ligand excluded by PLIP CL.44: 5 residues within 4Å: Chain D: V.44, L.179, N.180, Q.181, Y.182 Ligand excluded by PLIP

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

PX2.17: 6 residues within 4Å: Chain A: Q.233, W.237, I.389, P.392 Chain B: L.291, Y.298 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:L.291, A:W.237, A:W.237, A:I.389 Hydrogen bonds: B:Y.298

5 x R16: HEXADECANE(Non-covalent)

R16.18: 6 residues within 4Å: Chain B: I.224, W.231, F.429, S.430, W.437 Ligands: D10.19 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:W.231, B:F.429, B:W.437, B:W.437 R16.21: 4 residues within 4Å: Chain B: F.432, V.435, Y.439, Y.440 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.432, B:V.435, B:Y.439, B:Y.440 R16.41: 6 residues within 4Å: Chain C: I.214, L.222 Chain D: S.261, A.272, W.279, Y.285 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:I.214, C:L.222, D:W.279, D:W.279, D:Y.285 R16.45: 4 residues within 4Å: Chain E: I.216, W.231, F.429, W.437 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:I.216, E:W.231, E:F.429, E:W.437 R16.48: 4 residues within 4Å: Chain E: V.272, M.277, M.280, G.281 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:V.272, E:M.280

1 x A8W: Pregnenolone sulfate(Non-covalent)

A8W.28: 11 residues within 4Å: Chain A: V.248 Chain C: P.239, S.243, T.247, L.250 Chain D: P.244, V.248, T.252, L.255 Chain E: A.242, A.246 6 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: C:T.247, C:L.250, A:V.248, D:V.248, D:V.248, D:L.255

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

NAG.29: 3 residues within 4Å: Chain C: W.159, R.161, N.184 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.184 Water bridges: C:W.159

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kasaragod, V.B. et al., CryoEM structure of human full-length alpha1beta3gamma2L GABA(A)R in complex with pregnenolone sulfate. To Be Published

Release Date

2025-05-28

Peptides

Gamma-aminobutyric acid receptor subunit alpha-1: AD
Gamma-aminobutyric acid receptor subunit beta-3: BE
Isoform 1 of Gamma-aminobutyric acid receptor subunit gamma-2: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

B
B

E
E

C
C

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 1 of Gamma-aminobutyric acid receptor subunit gamma-2