SMTL ID : 9h9e.1

Cryo-EM structure of the human GABAA receptor alpha1 subunit in complex with the assembly factor NACHO/TMEM35A

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

2 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.1: 6 residues within 4Å: Chain A: F.155, V.163, A.164, H.165, N.166, Y.215 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.2: 6 residues within 4Å: Chain D: F.155, V.163, A.164, H.165, N.166, Y.215 No protein-ligand interaction detected (PLIP)

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

PX6.3: 19 residues within 4Å: Chain A: R.304, A.350, F.351, S.354, I.357, E.358, T.361, F.365, S.445, K.446, I.447, L.450, S.451, A.454, F.455, L.458 Chain C: F.92, L.96, L.99 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:E.358, A:T.361, A:F.365, A:L.450, A:F.455, A:F.455, A:L.458, C:L.99 Salt bridges: A:R.304, A:K.446 PX6.7: 19 residues within 4Å: Chain B: F.92, L.96, L.99 Chain D: R.304, A.350, F.351, S.354, I.357, E.358, T.361, F.365, S.445, K.446, I.447, L.450, S.451, A.454, F.455, L.458 8 PLIP interactions: 7 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:E.358, D:T.361, D:F.365, D:L.450, D:F.455, D:F.455, B:L.99 Salt bridges: D:R.304

2 x PC7: (7S)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSAN-1-AMINIUM 4-OXIDE(Non-covalent)

PC7.4: 18 residues within 4Å: Chain A: I.283, L.287, M.291, I.294 Chain B: P.111, L.112, I.123 Chain D: V.312, V.315, T.316, L.319, T.322, T.323, I.326, R.329, N.330, K.334 Ligands: PGT.5 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.287 Hydrogen bonds: B:L.112 PC7.8: 18 residues within 4Å: Chain A: V.312, V.315, T.316, L.319, T.322, T.323, I.326, R.329, N.330, K.334 Chain C: P.111, L.112, I.123 Chain D: I.283, L.287, M.291, I.294 Ligands: PGT.9 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D, 1 interactions with chain A Hydrogen bonds: C:L.112 Hydrophobic interactions: D:L.287, A:V.315

2 x PGT: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE(Non-covalent)

PGT.5: 15 residues within 4Å: Chain A: K.277, I.278, G.279, V.282, I.283, L.287, I.290, I.294, P.456, F.459, G.460, N.463, W.467, L.471 Ligands: PC7.4 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.278, A:V.282, A:I.290, A:I.294 Hydrogen bonds: A:K.277 Salt bridges: A:K.277 PGT.9: 15 residues within 4Å: Chain D: K.277, I.278, G.279, V.282, I.283, L.287, I.290, I.294, P.456, F.459, G.460, N.463, W.467, L.471 Ligands: PC7.8 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:I.278, D:V.282, D:I.290, D:I.294, D:F.459 Hydrogen bonds: D:K.277 Salt bridges: D:K.277

2 x CLR: CHOLESTEROL(Non-covalent)

CLR.6: 14 residues within 4Å: Chain A: E.199, A.338, T.339, A.340, W.343, Y.470 Chain C: A.50, L.51, P.52, L.53, L.54, F.103, F.104, L.107 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:W.343, A:W.343, A:W.343, A:W.343, C:L.51, C:L.53 Hydrogen bonds: A:T.339 CLR.10: 14 residues within 4Å: Chain B: A.50, L.51, P.52, L.53, L.54, F.103, F.104, L.107 Chain D: E.199, A.338, T.339, A.340, W.343, Y.470 8 PLIP interactions: 6 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: D:W.343, D:W.343, D:W.343, D:W.343, D:W.343, B:L.51, B:L.53 Hydrogen bonds: D:T.339

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hooda, Y. et al., Mechanism of NACHO-mediated assembly of pentameric ligand-gated ion channels. Biorxiv (2024)

Release Date

2024-12-04

Peptides

Gamma-aminobutyric acid receptor subunit alpha-1: AD
Novel acetylcholine receptor chaperone: BC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

B
B

C
C

Membrane

We predict this structure to be a membrane protein.
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Gamma-aminobutyric acid receptor subunit alpha-1

Novel acetylcholine receptor chaperone