SMTL ID : 8c2i.1

Transmembrane domain of resting state homomeric GluA1 AMPA receptor in complex with TARP gamma 3

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.70 Å

Oligo State

hetero-4-4-mer

Ligands

4 x PLM: PALMITIC ACID(Non-covalent)

PLM.1: 6 residues within 4Å: Chain A: L.540, Y.545, W.548, Y.555, F.606 Ligands: OLC.2 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.3: 8 residues within 4Å: Chain A: F.629 Chain B: L.540, Y.545, W.548, Y.555, L.603, F.606 Ligands: OLC.4 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.540, B:Y.545, B:W.548, B:Y.555, B:Y.555, B:L.603, B:F.606, A:F.629 PLM.7: 6 residues within 4Å: Chain C: L.540, Y.545, W.548, Y.555, F.606 Ligands: OLC.8 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.9: 8 residues within 4Å: Chain C: F.629 Chain D: L.540, Y.545, W.548, Y.555, L.603, F.606 Ligands: OLC.10 8 PLIP interactions: 7 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:L.540, D:Y.545, D:W.548, D:Y.555, D:Y.555, D:L.603, D:F.606, C:F.629

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

OLC.2: 10 residues within 4Å: Chain A: F.537, L.603, M.607, I.820 Chain D: I.622, G.625, V.626, F.629 Ligands: PLM.1, POV.13 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:I.820, D:F.629 OLC.4: 13 residues within 4Å: Chain A: R.621, I.622, G.625, F.629 Chain B: F.537, L.540, F.596, L.599, W.600, L.603, I.820 Ligands: PLM.3, POV.6 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.596, B:L.599, B:W.600, B:L.603, B:I.820, B:I.820, A:F.629 OLC.8: 9 residues within 4Å: Chain B: I.622, G.625, V.626, F.629 Chain C: F.537, L.603, M.607, I.820 Ligands: PLM.7 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:I.820, B:F.629, B:F.629 OLC.10: 14 residues within 4Å: Chain C: R.621, I.622, G.625, V.626, F.629 Chain D: F.537, L.540, F.596, L.599, W.600, L.603, I.820 Ligands: PLM.9, POV.12 9 PLIP interactions: 4 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: C:I.622, C:F.629, C:F.629, C:F.629, D:F.596, D:W.600, D:L.603, D:I.820, D:I.820

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

POV.5: 11 residues within 4Å: Chain B: G.535, V.536, F.537, Y.819, I.820, G.823, L.827 Chain F: T.92, A.93, L.97, F.106 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain F Hydrophobic interactions: B:F.537, B:Y.819, B:Y.819, B:L.827, F:F.106 POV.6: 8 residues within 4Å: Chain B: G.594, I.595, F.596, L.599 Chain G: I.190, V.193, H.197 Ligands: OLC.4 11 PLIP interactions: 8 interactions with chain B, 3 interactions with chain G Hydrophobic interactions: B:I.595, B:F.596, B:F.596, B:L.599, G:I.190, G:V.193 Hydrogen bonds: B:I.595, B:F.596 Water bridges: B:G.594, B:N.597 Salt bridges: G:H.197 POV.11: 12 residues within 4Å: Chain C: V.626 Chain D: G.535, V.536, F.537, Y.819, I.820, G.823, G.824, L.827 Chain H: A.93, L.97, I.150 6 PLIP interactions: 1 interactions with chain C, 1 interactions with chain H, 4 interactions with chain D Hydrophobic interactions: C:V.626, H:I.150, D:Y.819, D:Y.819, D:I.820, D:L.827 POV.12: 7 residues within 4Å: Chain D: I.556, G.594, I.595, F.596 Chain E: I.190, H.197 Ligands: OLC.10 13 PLIP interactions: 9 interactions with chain D, 4 interactions with chain E Hydrophobic interactions: D:I.556, D:I.595, D:F.596, D:F.596, D:F.596, E:I.190, E:I.190 Hydrogen bonds: D:I.595, D:F.596 Water bridges: D:G.594, D:N.597 Salt bridges: E:H.197, E:H.197 POV.13: 11 residues within 4Å: Chain A: V.536, F.537, Y.819, I.820, G.823, G.824 Chain D: V.626 Chain E: A.93, L.97, V.154 Ligands: OLC.2 5 PLIP interactions: 3 interactions with chain A, 1 interactions with chain D, 1 interactions with chain E Hydrophobic interactions: A:F.537, A:Y.819, A:I.820, D:V.626, E:V.154 POV.14: 8 residues within 4Å: Chain A: I.556, I.595, F.596, L.599 Chain F: I.190, V.193, V.194, H.197 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain F Hydrophobic interactions: A:I.556, A:I.595, A:F.596, A:F.596, A:L.599, F:I.190 Salt bridges: F:H.197 POV.15: 9 residues within 4Å: Chain B: V.626 Chain C: V.536, F.537, Y.819, I.820 Chain G: A.93, L.97, V.100, V.154 7 PLIP interactions: 4 interactions with chain C, 2 interactions with chain G, 1 interactions with chain B Hydrophobic interactions: C:F.537, C:Y.819, C:Y.819, C:I.820, G:V.100, G:V.154, B:V.626 POV.16: 8 residues within 4Å: Chain C: I.556, I.595, F.596, L.599 Chain H: I.190, V.193, V.194, H.197 6 PLIP interactions: 2 interactions with chain H, 4 interactions with chain C Hydrophobic interactions: H:I.190, C:I.556, C:I.595, C:F.596, C:L.599 Salt bridges: H:H.197

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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