SMTL ID : 8c2h.1

Transmembrane domain of active state homomeric GluA1 AMPA receptor in tandem with TARP gamma 3

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.64 Å

Oligo State

hetero-4-4-mer

Ligands

6 x PLM: PALMITIC ACID(Non-covalent)

PLM.1: 5 residues within 4Å: Chain A: W.548, Y.555, F.606 Chain D: F.629 Ligands: OLC.2 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:W.548, A:Y.555, A:F.606, A:F.606, D:F.629 PLM.3: 6 residues within 4Å: Chain A: V.626 Chain B: Y.819, G.823, G.824, L.827 Ligands: PLM.10 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.819, B:L.827, A:V.626 PLM.5: 5 residues within 4Å: Chain B: F.629 Chain C: W.548, Y.555, F.606 Ligands: OLC.6 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:W.548, C:Y.555, C:F.606, C:F.606, B:F.629 PLM.7: 7 residues within 4Å: Chain C: V.626 Chain D: Y.819, G.823, G.824, L.827 Ligands: OLC.8, PLM.12 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:Y.819, D:L.827, C:V.626 PLM.10: 6 residues within 4Å: Chain B: V.536, Y.819 Chain F: A.93, F.106, I.150 Ligands: PLM.3 5 PLIP interactions: 2 interactions with chain F, 3 interactions with chain B Hydrophobic interactions: F:F.106, F:I.150, B:Y.819, B:Y.819, B:Y.819 PLM.12: 6 residues within 4Å: Chain D: V.536, Y.819, G.823 Chain H: A.93, I.150 Ligands: PLM.7 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain H Hydrophobic interactions: D:Y.819, D:Y.819, H:I.150

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

OLC.2: 9 residues within 4Å: Chain A: F.537, F.596, I.820 Chain D: R.621, G.625, V.626, F.629 Ligands: PLM.1, POV.9 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:F.596, A:I.820, A:I.820, D:V.626, D:F.629 OLC.4: 8 residues within 4Å: Chain A: R.621, G.625, F.629 Chain B: F.537, F.596, W.600, L.603, I.820 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:F.537, B:F.596, B:W.600, B:L.603, B:I.820, A:R.621, A:F.629, A:F.629 OLC.6: 8 residues within 4Å: Chain B: G.625, V.626, F.629 Chain C: F.537, F.596, I.820 Ligands: PLM.5, POV.11 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:F.596, C:I.820, C:I.820, B:V.626, B:F.629 OLC.8: 9 residues within 4Å: Chain C: R.621, G.625, F.629 Chain D: F.537, F.596, W.600, L.603, I.820 Ligands: PLM.7 9 PLIP interactions: 5 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:F.537, D:F.596, D:W.600, D:L.603, D:I.820, C:R.621, C:F.629, C:F.629, C:F.629

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

POV.9: 14 residues within 4Å: Chain A: V.536, F.537, Y.819, I.820, G.823, G.824, G.826, L.827 Chain D: V.626 Chain E: A.93, L.96, L.97, I.150 Ligands: OLC.2 9 PLIP interactions: 6 interactions with chain A, 2 interactions with chain E, 1 interactions with chain D Hydrophobic interactions: A:F.537, A:Y.819, A:Y.819, A:L.827, A:L.827, E:I.150, D:V.626 Hydrogen bonds: A:Y.819, E:T.92 POV.11: 14 residues within 4Å: Chain B: V.626 Chain C: V.536, F.537, Y.819, I.820, G.823, G.824, G.826, L.827 Chain G: A.93, L.96, L.97, I.150 Ligands: OLC.6 8 PLIP interactions: 2 interactions with chain G, 5 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: G:I.150, C:F.537, C:Y.819, C:Y.819, C:L.827, B:V.626 Hydrogen bonds: G:T.92, C:Y.819

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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