SMTL ID : 8pet.1

Cryo-EM structure of the full-length human alpha1beta3 GABA(A) receptor (babba arrangement) in complex with nanobody Nb25, expressed with a 5-fold excess of beta3 over alpha1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-3-1-mer

Ligands

5 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: 10 residues within 4Å: Chain A: N.143, N.166, T.168, M.169, P.170 Chain B: R.126, D.129, K.152 Chain D: L.144, S.147 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.129 NAG-NAG-BMA-MAN-MAN.2: 13 residues within 4Å: Chain B: N.189, T.191, E.230, H.231, R.232, V.234, S.235, R.236, N.237, S.249, S.251, F.252, R.253 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.232, B:R.236 NAG-NAG-BMA-MAN-MAN.4: 13 residues within 4Å: Chain C: N.189, T.191, E.230, H.231, R.232, V.234, S.235, R.236, N.237, S.249, S.251, F.252, R.253 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.232 NAG-NAG-BMA-MAN-MAN.6: 12 residues within 4Å: Chain C: I.65, R.126, D.129, Q.130 Chain D: N.142, N.143, L.144, N.166, M.169, P.170 Chain E: I.65, D.129 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:D.129, D:N.143, C:D.129 Hydrophobic interactions: D:N.143 NAG-NAG-BMA-MAN-MAN.7: 20 residues within 4Å: Chain E: N.189, T.191, E.230, H.231, R.232, V.234, S.235, R.236, N.237, S.249, S.251, F.252, R.253 Chain F: N.30, Y.31, G.100, R.101, S.103, T.110, D.113 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:N.237, E:R.232, E:R.236, F:Y.31

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.3: 4 residues within 4Å: Chain B: P.118, L.119, N.120, H.159 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain C: P.118, L.119, N.120, H.159 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain E: P.118, L.119, N.120, H.159 No protein-ligand interaction detected (PLIP)

2 x R16: HEXADECANE(Non-covalent)

R16.9: 13 residues within 4Å: Chain A: I.278, V.282, L.287, I.290, I.294, Q.297, P.456, F.459, G.460, N.463, W.467, L.471 Ligands: D10.11 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.278, A:I.290, A:F.459 R16.21: 14 residues within 4Å: Chain D: I.278, V.282, Y.286, L.287, I.290, I.294, Q.297, P.456, F.459, G.460, N.463, W.467, L.471 Ligands: D10.16 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:I.290, D:P.456, D:F.459, D:W.467

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.10: 16 residues within 4Å: Chain A: R.304, I.357, E.358, T.361, V.362, F.365, K.367, R.368, N.442, S.443, S.445, K.446, I.447, L.450, S.451, F.455 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:T.361, A:K.446, A:I.447, A:L.450 Hydrogen bonds: A:R.304, A:R.304, A:S.443, A:S.443, A:S.443, A:K.446 Salt bridges: A:R.304, A:K.367, A:K.367, A:R.368, A:K.446, A:K.446 PIO.22: 17 residues within 4Å: Chain D: R.304, I.357, E.358, T.361, F.365, K.367, R.368, N.442, S.443, S.445, K.446, I.447, L.450, S.451, A.454, F.455 Ligands: D10.14 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:T.361, D:I.447, D:L.450 Hydrogen bonds: D:R.304, D:R.304, D:N.442, D:S.443, D:S.443, D:K.446 Salt bridges: D:R.304, D:K.367, D:K.367, D:R.368, D:K.446, D:K.446

12 x D10: DECANE(Non-covalent)

D10.11: 10 residues within 4Å: Chain A: I.294, Q.297, V.298, W.301, P.456 Chain B: L.337, A.340, F.341, Y.344 Ligands: R16.9 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.341, B:F.341, B:Y.344, A:V.298, A:W.301 D10.12: 9 residues within 4Å: Chain B: I.270, I.274, W.277, Y.324, P.474, F.477, S.478, N.481, W.485 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.270, B:W.277, B:F.477 D10.13: 9 residues within 4Å: Chain A: I.283 Chain B: M.323, M.326, G.327, V.330, F.331, L.334, T.476, F.480 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:V.330, B:F.331, B:F.331, B:L.334, B:T.476 D10.14: 10 residues within 4Å: Chain B: I.274, W.277, V.278, W.281 Chain D: I.357, A.360, T.361, Y.364, F.365 Ligands: PIO.22 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: B:W.281, D:I.357, D:Y.364 D10.16: 10 residues within 4Å: Chain C: L.337, A.340, F.341, Y.344, R.349 Chain D: I.294, Q.297, V.298, W.301 Ligands: R16.21 6 PLIP interactions: 2 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:Y.344, C:Y.344, D:V.298, D:W.301, D:W.301, D:W.301 D10.17: 10 residues within 4Å: Chain C: I.270, I.274, W.277, Y.324, P.474, F.477, S.478, N.481, W.485 Ligands: D10.18 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:I.270, C:W.277, C:W.485 D10.18: 9 residues within 4Å: Chain C: W.277, W.281, R.467, R.470, I.471, P.474 Chain E: Y.344 Ligands: D10.17, D10.20 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:I.471, C:P.474 D10.19: 9 residues within 4Å: Chain C: M.323, M.326, G.327, V.330, F.331, L.334, T.476, F.480 Chain D: I.283 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:M.326, C:V.330, C:F.331, C:L.334, C:T.476 D10.20: 11 residues within 4Å: Chain C: I.274, W.277, V.278, W.281, P.474 Chain E: L.337, A.340, F.341, Y.344, R.349 Ligands: D10.18 9 PLIP interactions: 5 interactions with chain E, 4 interactions with chain C Hydrophobic interactions: E:L.337, E:A.340, E:F.341, E:F.341, E:Y.344, C:W.277, C:V.278, C:W.281, C:W.281 D10.23: 9 residues within 4Å: Chain A: I.357, A.360, T.361, Y.364, F.365 Chain E: I.274, W.277, V.278, W.281 6 PLIP interactions: 3 interactions with chain E, 3 interactions with chain A Hydrophobic interactions: E:V.278, E:W.281, E:W.281, A:A.360, A:Y.364, A:Y.364 D10.24: 9 residues within 4Å: Chain E: I.262, I.270, I.274, W.277, P.474, F.477, S.478, N.481, W.485 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:I.270, E:W.277, E:P.474, E:W.485 D10.25: 10 residues within 4Å: Chain C: L.263, M.267 Chain E: M.323, M.326, G.327, V.330, F.331, L.334, T.476, F.480 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:V.330, E:V.330, E:F.331, E:T.476

1 x ZN: ZINC ION(Non-covalent)

ZN.15: 4 residues within 4Å: Chain B: H.307, E.310 Chain C: H.307 Chain E: H.307 3 PLIP interactions: 1 interactions with chain E, 1 interactions with chain C, 1 interactions with chain B Metal complexes: E:H.307, C:H.307, B:H.307

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sente, A. et al., Subunit abundance shapes GABAA receptor stoichiometry. To Be Published

Release Date

2025-07-02

Peptides

Gamma-aminobutyric acid receptor subunit alpha-1: AD
Gamma-aminobutyric acid receptor subunit beta-3: BCE
Nanobody Nb25: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
C

B
B

C
D

E
E

F
F

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

Nanobody Nb25

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