SMTL ID : 9eqg.1

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

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: 18 residues within 4Å: Chain A: N.146, T.148 Chain B: K.137 Chain C: S.139, N.140, G.143, K.144, A.158, D.159, W.162, P.166 Chain D: N.63, S.127, A.144, N.146, P.150, K.152 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.4 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:D.159 Water bridges: B:G.133

3 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: 6 residues within 4Å: Chain B: N.174, R.217, S.220, R.221, S.236, R.238 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.217 NAG-NAG-BMA-MAN-MAN-MAN.4: 8 residues within 4Å: Chain D: N.146, M.149, P.150 Chain E: D.114, Q.115 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: 2 interactions with chain E Hydrogen bonds: E:D.114, E:D.114 NAG-NAG-BMA-MAN-MAN-MAN.5: 6 residues within 4Å: Chain E: N.174, R.217, S.220, R.221, S.236, R.238 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:R.221 Water bridges: E:S.234

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.103, N.105, H.144 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.6: 2 residues within 4Å: Chain E: N.105, H.144 No protein-ligand interaction detected (PLIP)

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

PGW.7: 10 residues within 4Å: Chain A: K.257, I.258, G.259, I.263, I.274 Chain B: P.301, M.311, F.314, L.322 Ligands: R16.12 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.263, A:I.274, B:F.314, B:L.322 Hydrogen bonds: A:I.258, A:G.259 PGW.33: 14 residues within 4Å: Chain D: K.257, I.258, G.259, V.262, L.267, I.270, F.439, N.443, W.447 Chain E: N.290, M.311, F.314, V.315 Ligands: D10.35 12 PLIP interactions: 10 interactions with chain D, 2 interactions with chain E Hydrophobic interactions: D:V.262, D:V.262, D:L.267, D:I.270, D:F.439, D:N.443, D:W.447, D:W.447, E:F.314, E:V.315 Hydrogen bonds: D:I.258, D:G.259

11 x D10: DECANE

D10.8: 3 residues within 4Å: Chain E: I.259 Ligands: PT5.11, PLM.16 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:I.259 D10.9: 4 residues within 4Å: Chain A: L.444, W.447, N.452 Ligands: R16.12 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.447 D10.15: 4 residues within 4Å: Chain A: V.278, W.281 Chain B: F.326, Y.329 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:F.326, B:Y.329, A:V.278, A:W.281, A:W.281 D10.19: 3 residues within 4Å: Chain B: S.461, L.465 Ligands: R16.18 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.465 D10.24: 1 residues within 4Å: Chain C: S.330 No protein-ligand interaction detected (PLIP) D10.26: 3 residues within 4Å: Chain B: W.266 Chain C: Y.358, F.359 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Y.358, C:F.359 D10.28: 3 residues within 4Å: Chain C: L.337, V.467, S.471 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.337, C:V.467 D10.35: 2 residues within 4Å: Chain D: L.444 Ligands: PGW.33 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:L.444, D:L.444 D10.36: 2 residues within 4Å: Chain D: T.449, Y.450 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:T.449, D:Y.450 D10.42: 2 residues within 4Å: Chain E: W.468, V.472 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:V.472 D10.44: 4 residues within 4Å: Chain E: W.266, R.450, I.454 Ligands: PLM.16 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:W.266, E:R.450, E:I.454

10 x HEX: HEXANE

HEX.10: 3 residues within 4Å: Chain A: W.281, R.432, I.433 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.281 HEX.13: 2 residues within 4Å: Chain A: W.323, Y.450 No protein-ligand interaction detected (PLIP) HEX.14: 3 residues within 4Å: Chain A: Y.329 Chain E: L.248, M.252 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.329 HEX.21: 1 residues within 4Å: Chain B: M.311 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:M.311 HEX.23: 2 residues within 4Å: Chain B: W.266, I.454 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:W.266, B:I.454 HEX.27: 5 residues within 4Å: Chain B: M.252, L.256 Chain C: S.340, F.343, I.344 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:F.343, C:I.344, B:L.256 HEX.30: 3 residues within 4Å: Chain C: R.454, I.455 Ligands: PLM.34 No protein-ligand interaction detected (PLIP) HEX.43: 3 residues within 4Å: Chain E: L.319, E.323, F.326 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:E.323, E:F.326 HEX.46: 1 residues within 4Å: Chain E: G.312 No protein-ligand interaction detected (PLIP) HEX.47: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

2 x PT5: [(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phospho ryl]oxy-propan-2-yl] (8Z)-icosa-5,8,11,14-tetraenoate

PT5.11: 22 residues within 4Å: Chain A: R.284, A.330, F.331, F.333, S.334, I.337, E.338, T.341, F.345, K.347, R.348, K.361, N.422, S.423, S.425, K.426, I.427, L.430, S.431, F.435, L.438 Ligands: D10.8 28 PLIP interactions: 28 interactions with chain A Hydrophobic interactions: A:A.330, A:F.331, A:F.333, A:I.337, A:E.338, A:T.341, A:K.426, A:I.427, A:I.427, A:L.430, A:F.435, A:F.435, A:F.435, A:L.438 Hydrogen bonds: A:R.284, A:R.284, A:S.423, A:S.423, A:S.425, A:K.426 Salt bridges: A:R.284, A:K.347, A:K.347, A:R.348, A:K.361, A:K.361, A:K.426, A:K.426 PT5.38: 18 residues within 4Å: Chain D: R.284, A.330, S.334, E.338, F.345, K.347, R.348, K.361, N.422, S.423, S.425, K.426, I.427, L.430, S.431, A.434, F.435, L.438 25 PLIP interactions: 25 interactions with chain D Hydrophobic interactions: D:A.330, D:E.338, D:E.338, D:F.345, D:I.427, D:L.430, D:L.430, D:A.434, D:F.435, D:F.435, D:F.435, D:L.438 Hydrogen bonds: D:R.284, D:S.423, D:S.423, D:S.425, D:K.426 Salt bridges: D:R.284, D:K.347, D:K.347, D:R.348, D:K.361, D:K.361, D:K.426, D:K.426

5 x R16: HEXADECANE

R16.12: 8 residues within 4Å: Chain A: I.258, I.270, F.439, N.443, W.447, L.451 Ligands: PGW.7, D10.9 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.258, A:I.270, A:F.439, A:W.447, A:L.451, A:L.451 R16.18: 3 residues within 4Å: Chain B: I.243, W.468 Ligands: D10.19 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.243, B:W.468, B:W.468 R16.20: 5 residues within 4Å: Chain B: L.462, F.463, V.466, Y.470, Y.471 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.462, B:F.463, B:V.466, B:Y.470, B:Y.470, B:Y.471 R16.31: 8 residues within 4Å: Chain C: G.273, I.277, L.285 Chain D: S.305, A.318, W.323, A.326, Y.329 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:A.318, D:W.323, D:Y.329, C:I.277, C:L.285 R16.41: 5 residues within 4Å: Chain E: I.247, W.262, F.460, N.464, W.468 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:I.247, E:W.262, E:F.460

3 x PLM: PALMITIC ACID

PLM.16: 6 residues within 4Å: Chain A: I.337, T.341, Y.344 Chain E: W.266 Ligands: D10.8, D10.44 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain E Hydrophobic interactions: A:I.337, A:Y.344, E:W.266, E:W.266 PLM.25: 8 residues within 4Å: Chain C: M.272, T.276, T.284, W.291, C.462, N.465, W.469, L.473 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:T.276, C:T.284, C:W.291, C:W.469 PLM.34: 6 residues within 4Å: Chain C: V.292, W.295 Chain D: I.337, T.341, Y.344 Ligands: HEX.30 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:I.337, D:Y.344, C:V.292, C:W.295, C:W.295 Hydrogen bonds: D:Y.344

3 x CL: CHLORIDE ION

CL.17: 6 residues within 4Å: Chain A: P.87, V.88, L.223, N.224, Q.225, Y.226 Ligand excluded by PLIP CL.32: 4 residues within 4Å: Chain C: P.103, V.104, Y.238, Q.239 Ligand excluded by PLIP CL.40: 5 residues within 4Å: Chain D: V.88, L.223, N.224, Q.225, Y.226 Ligand excluded by PLIP

2 x ABU: GAMMA-AMINO-BUTANOIC ACID

ABU.22: 11 residues within 4Å: Chain A: F.100, R.102, L.153, T.165 Chain B: Y.122, E.180, S.181, Y.182, F.225, T.227, Y.230 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:F.225, B:Y.230, A:F.100, A:L.153 Hydrogen bonds: B:S.181, B:Y.230, B:Y.230 Salt bridges: A:R.102 ABU.45: 10 residues within 4Å: Chain D: F.100, R.102, T.165 Chain E: Y.122, E.180, S.181, Y.182, F.225, T.227, Y.230 9 PLIP interactions: 5 interactions with chain E, 4 interactions with chain D Hydrophobic interactions: E:Y.230, D:F.100 Hydrogen bonds: E:E.180, E:Y.182, E:T.227, E:Y.230, D:T.165, D:T.165 Salt bridges: D:R.102

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose

NAG.29: 5 residues within 4Å: Chain C: W.222, K.223, L.245, R.246, N.247 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.247

1 x 01: Puerarin

01.37: 16 residues within 4Å: Chain C: D.95, M.96, Y.97, N.99, F.116, A.118, T.181, R.183 Chain D: H.137, Y.195, V.238, Q.239, S.240, S.241, T.242, Y.245 15 PLIP interactions: 6 interactions with chain D, 9 interactions with chain C Hydrogen bonds: D:H.137, D:H.137, D:S.240, D:T.242, C:D.95, C:D.95, C:R.183 Water bridges: D:H.137, C:M.96 pi-Stacking: D:Y.245 Hydrophobic interactions: C:Y.97, C:F.116, C:F.116, C:A.118, C:T.181

1 x PX2: 1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE

PX2.39: 3 residues within 4Å: Chain D: W.281, I.433 Chain E: Y.329 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain E Hydrophobic interactions: D:W.281, D:W.281, D:W.281, D:W.281, D:I.433 Hydrogen bonds: E:Y.329

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lyu, Q. et al., A brain-to-gut signal controls intestinal fat absorption. Nature (2024)

Release Date

2024-09-18

Peptides

Gamma-aminobutyric acid receptor subunit alpha-1: AD
Gamma-aminobutyric acid receptor subunit beta-3: BE
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

Gamma-aminobutyric acid receptor subunit gamma-2

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