SMTL ID : 7qn5.1

Cryo-EM structure of human full-length extrasynaptic alpha4beta3delta GABA(A)R in complex with nanobody Nb25

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-3-1-2-mer

Ligands

4 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.1: 5 residues within 4Å: Chain A: M.122, T.125, N.144, P.148 Chain C: D.114 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:M.122 NAG-NAG-BMA-MAN-MAN.3: 8 residues within 4Å: Chain B: N.174, R.217, V.219, S.220, R.221, S.236, F.237, R.238 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.217, B:R.221 NAG-NAG-BMA-MAN-MAN.5: 12 residues within 4Å: Chain C: N.174, R.217, V.219, S.220, R.221, S.236, R.238 Chain F: N.28, Y.29, S.101, T.108, D.111 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain F Hydrogen bonds: C:R.217, C:R.217, C:R.221, F:Y.29, F:Y.29, F:D.111 NAG-NAG-BMA-MAN-MAN.7: 12 residues within 4Å: Chain D: N.174, R.217, V.219, S.220, R.221, S.236, R.238 Chain G: N.28, Y.29, S.101, T.108, D.111 6 PLIP interactions: 3 interactions with chain G, 3 interactions with chain D Hydrogen bonds: G:T.108, D:R.217, D:R.217, D:R.221, G:Y.29, G:Y.29, G:D.111

3 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 3 residues within 4Å: Chain B: P.103, N.105, H.144 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain C: P.103, N.105, H.144 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain D: P.103, N.105, H.144 No protein-ligand interaction detected (PLIP)

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

NAG.8: 4 residues within 4Å: Chain A: I.104, M.155, N.157, T.159 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.104 Hydrogen bonds: A:T.159, A:T.159 NAG.17: 4 residues within 4Å: Chain E: N.65, V.193, Y.194, Y.195 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.65, E:Y.194 NAG.18: 1 residues within 4Å: Chain E: N.103 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.103

1 x PX6: 1,2-DIPALMITOYL-SN-GLYCERO-3-PHOSPHATE(Non-covalent)

PX6.9: 14 residues within 4Å: Chain A: A.328, F.329, S.332, E.336, A.339, F.343, Q.347, S.516, K.517, I.518, Y.521, L.525, F.526, T.529 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.329, A:F.329, A:E.336, A:A.339, A:F.343, A:Y.521, A:Y.521, A:L.525, A:F.526 Hydrogen bonds: A:S.516, A:K.517 Salt bridges: A:K.517

2 x D10: DECANE(Non-covalent)

D10.10: 4 residues within 4Å: Chain A: W.279 Chain B: L.322, A.325, Y.329 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:W.279, A:W.279, B:L.322, B:A.325, B:Y.329 D10.19: 6 residues within 4Å: Chain A: I.335, A.338, A.339, Y.342, F.343 Chain E: W.270 6 PLIP interactions: 2 interactions with chain E, 4 interactions with chain A Hydrophobic interactions: E:W.270, E:W.270, A:I.335, A:A.338, A:Y.342, A:F.343

2 x OCT: N-OCTANE(Non-covalent)

OCT.11: 5 residues within 4Å: Chain A: A.316, D.320, W.321, A.324 Chain E: V.249 6 PLIP interactions: 2 interactions with chain E, 4 interactions with chain A Hydrophobic interactions: E:V.249, E:V.249, A:A.316, A:D.320, A:W.321, A:A.324 OCT.20: 4 residues within 4Å: Chain E: I.316, V.442, A.449, Y.450 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:I.316, E:V.442

2 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.12: 12 residues within 4Å: Chain B: N.66, D.68, Y.87, Q.89 Chain C: Y.122, E.180, S.181, Y.182, F.225, A.226, T.227, Y.230 13 PLIP interactions: 6 interactions with chain B, 7 interactions with chain C Hydrogen bonds: B:N.66, B:Q.89, B:Q.89, B:T.201, B:T.201, C:Y.122, C:E.180, C:A.226, C:T.227, C:T.227 Salt bridges: B:D.68 pi-Cation interactions: C:Y.182, C:F.225 EPE.15: 11 residues within 4Å: Chain C: D.68, Y.87, Q.89 Chain D: Y.122, E.180, S.181, Y.182, F.225, A.226, T.227, Y.230 10 PLIP interactions: 7 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:Y.122, D:E.180, D:A.226, D:T.227, D:T.227, C:Q.89 pi-Cation interactions: D:Y.182, D:F.225 Water bridges: C:T.201 Salt bridges: C:D.68

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

CL.13: 4 residues within 4Å: Chain C: F.130, H.132, G.133 Chain D: S.129 Ligand excluded by PLIP CL.14: 5 residues within 4Å: Chain B: F.130, H.132, G.133 Chain C: K.128, S.129 Ligand excluded by PLIP CL.16: 4 residues within 4Å: Chain D: F.130, H.132 Chain E: S.131, A.132 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sente, A. et al., Differential assembly diversifies GABA A receptor structures and signalling. Nature (2022)

Release Date

2022-04-13

Peptides

Gamma-aminobutyric acid receptor subunit alpha-4: A
Gamma-aminobutyric acid receptor subunit beta-3: BCD
Gamma-aminobutyric acid receptor subunit delta: E
Nanobody Nb25: FG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

Membrane

We predict this structure to be a membrane protein.
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Gamma-aminobutyric acid receptor subunit alpha-4

Gamma-aminobutyric acid receptor subunit beta-3

Gamma-aminobutyric acid receptor subunit delta

Nanobody Nb25

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