SMTL ID : 8c1q.1

Resting state homomeric GluA1 AMPA receptor in complex with TARP gamma 3

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.82 Å

Oligo State

hetero-4-4-mer

Ligands

4 x ZK1: {[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2H)-yl]methyl}phosphonic acid(Non-covalent)

ZK1.1: 15 residues within 4Å: Chain A: E.424, Y.427, Y.472, P.500, L.501, T.502, R.507, L.672, G.675, S.676, T.708, E.727, T.729, M.730, Y.754 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.472 Hydrogen bonds: A:P.500, A:T.502, A:T.502, A:R.507, A:R.507, A:S.676, A:S.676, A:S.676 pi-Stacking: A:Y.472 Halogen bonds: A:T.729 ZK1.4: 11 residues within 4Å: Chain B: Y.427, Y.472, P.500, L.501, T.502, R.507, G.675, S.676, T.729, M.730, Y.754 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Y.472 Hydrogen bonds: B:P.500, B:T.502, B:T.502, B:R.507, B:S.676 pi-Stacking: B:Y.472 ZK1.7: 14 residues within 4Å: Chain C: E.424, Y.427, Y.472, P.500, L.501, T.502, R.507, L.672, G.675, S.676, T.708, E.727, M.730, Y.754 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:Y.472, C:Y.472 Hydrogen bonds: C:P.500, C:T.502, C:T.502, C:R.507, C:R.507, C:A.674, C:S.676 pi-Stacking: C:Y.472 ZK1.10: 14 residues within 4Å: Chain D: E.424, Y.427, Y.472, P.500, L.501, T.502, R.507, G.675, S.676, T.708, E.727, T.729, M.730, Y.754 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:Y.472, D:Y.472 Hydrogen bonds: D:P.500, D:T.502, D:T.502, D:R.507, D:R.507, D:S.676, D:S.676, D:S.676, D:T.708, D:E.727, D:K.752 pi-Stacking: D:Y.472 pi-Cation interactions: D:K.752 Halogen bonds: D:T.729

4 x PLM: PALMITIC ACID(Non-covalent)

PLM.2: 6 residues within 4Å: Chain A: L.540, Y.545, W.548, Y.555, F.606 Ligands: OLC.3 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.540, A:Y.545, A:W.548, A:Y.555, A:F.606, A:F.606 PLM.5: 8 residues within 4Å: Chain A: F.629 Chain B: L.540, Y.545, W.548, Y.555, L.603, F.606 Ligands: OLC.6 11 PLIP interactions: 1 interactions with chain A, 10 interactions with chain B Hydrophobic interactions: A:F.629, B:L.540, B:Y.545, B:W.548, B:W.548, B:Y.555, B:Y.555, B:L.603, B:F.606, B:F.606, B:F.606 PLM.8: 6 residues within 4Å: Chain C: L.540, Y.545, W.548, Y.555, F.606 Ligands: OLC.9 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:L.540, C:Y.545, C:W.548, C:Y.555, C:F.606, C:F.606 PLM.11: 8 residues within 4Å: Chain C: F.629 Chain D: L.540, Y.545, W.548, Y.555, L.603, F.606 Ligands: OLC.12 11 PLIP interactions: 10 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:L.540, D:Y.545, D:W.548, D:W.548, D:Y.555, D:Y.555, D:L.603, D:F.606, D:F.606, D:F.606, C:F.629

4 x OLC: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate(Non-covalent)

OLC.3: 11 residues within 4Å: Chain A: F.537, F.596, L.603, I.820 Chain D: I.622, G.625, V.626, F.629 Ligands: PLM.2, POV.13, POV.14 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:F.596, A:I.820, D:V.626, D:F.629 OLC.6: 13 residues within 4Å: Chain A: R.621, I.622, G.625, V.626, F.629 Chain B: F.537, L.540, F.596, L.599, W.600, I.820 Ligands: PLM.5, POV.15 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.596, B:L.599, B:I.820, B:I.820, A:F.629, A:F.629 OLC.9: 10 residues within 4Å: Chain B: I.622, G.625, V.626, F.629 Chain C: F.537, L.603, I.820 Ligands: PLM.8, POV.16, POV.17 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:F.537, C:L.603, C:I.820, C:I.820, B:V.626, B:F.629 OLC.12: 12 residues within 4Å: Chain C: R.621, I.622, G.625, F.629 Chain D: F.537, L.540, F.596, L.599, W.600, I.820 Ligands: PLM.11, POV.18 6 PLIP interactions: 2 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:F.629, C:F.629, D:F.596, D:L.599, D:I.820, D:I.820

6 x POV: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate(Non-covalent)

POV.13: 12 residues within 4Å: Chain A: G.535, V.536, F.537, Y.819, I.820, G.823 Chain D: V.626 Chain E: T.92, A.93, L.96, V.154 Ligands: OLC.3 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:Y.819, D:V.626 POV.14: 8 residues within 4Å: Chain A: I.595, F.596, L.599 Chain F: I.190, V.193, V.194, H.197 Ligands: OLC.3 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain F Hydrophobic interactions: A:I.595, A:F.596, A:F.596, A:L.599, F:I.190 Salt bridges: F:H.197 POV.15: 13 residues within 4Å: Chain A: V.626 Chain B: V.536, F.537, Y.819, I.820, G.823, G.824, L.827 Chain F: T.92, A.93, L.96, L.97 Ligands: OLC.6 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.537, B:Y.819, B:L.827, A:V.626 POV.16: 12 residues within 4Å: Chain C: G.535, V.536, F.537, Y.819, I.820, G.823, G.824 Chain G: T.92, A.93, L.96, V.154 Ligands: OLC.9 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.819 POV.17: 8 residues within 4Å: Chain C: I.595, F.596, L.599 Chain H: I.190, V.193, V.194, H.197 Ligands: OLC.9 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain H Hydrophobic interactions: C:I.595, C:F.596, C:F.596, C:L.599, H:I.190 Salt bridges: H:H.197, H:H.197 POV.18: 13 residues within 4Å: Chain C: V.626 Chain D: V.536, F.537, Y.819, I.820, G.823, G.824, L.827 Chain H: T.92, A.93, L.97, F.106 Ligands: OLC.12 5 PLIP interactions: 3 interactions with chain D, 1 interactions with chain H, 1 interactions with chain C Hydrophobic interactions: D:F.537, D:Y.819, D:L.827, H:F.106, C:V.626

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, D. et al., Structural mobility tunes signalling of the GluA1 AMPA glutamate receptor. Nature (2023)

Release Date

2023-08-30

Peptides

Glutamate receptor 1 flip isoform: ABCD
Voltage-dependent calcium channel gamma-3 subunit: EFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

Membrane

We predict this structure to be a membrane protein.
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Glutamate receptor 1 flip isoform

Voltage-dependent calcium channel gamma-3 subunit

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