SMTL ID : 8c1p.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.90 Å

Oligo State

hetero-4-4-mer

Ligands

4 x CYZ: CYCLOTHIAZIDE(Non-covalent)

CYZ.1: 13 residues within 4Å: Chain A: K.515, P.516, F.517, M.518, S.519, L.773, S.776, L.781, D.782 Chain D: I.503, S.751, K.752, G.753 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: A:K.515, A:L.773, A:L.781, D:I.503, D:I.503, D:K.752 Hydrogen bonds: A:S.519, A:S.776, A:S.776 CYZ.5: 14 residues within 4Å: Chain B: K.515, P.516, F.517, M.518, S.519, L.773, S.776, L.781, D.782, K.785 Chain C: I.503, S.751, K.752, G.753 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:K.515, B:L.773, C:I.503, C:I.503 Hydrogen bonds: B:S.519, B:S.776, B:S.776, C:S.751, C:S.751 CYZ.10: 13 residues within 4Å: Chain B: I.503, S.751, K.752, G.753 Chain C: K.515, P.516, F.517, M.518, S.519, L.773, S.776, L.781, D.782 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:K.515, C:L.773, C:L.781, B:I.503, B:I.503 Hydrogen bonds: C:S.519, C:S.776, C:S.776 CYZ.14: 13 residues within 4Å: Chain A: I.503, S.751, K.752, G.753 Chain D: K.515, P.516, M.518, S.519, L.773, S.776, L.781, D.782, K.785 8 PLIP interactions: 5 interactions with chain D, 3 interactions with chain A Hydrophobic interactions: D:K.515, D:L.773, A:I.503, A:I.503 Hydrogen bonds: D:S.519, D:S.776, D:S.776, A:S.751

6 x PLM: PALMITIC ACID(Non-covalent)

PLM.2: 4 residues within 4Å: Chain A: W.548, Y.555, F.606 Chain D: F.629 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:Y.555, A:F.606, D:F.629 PLM.6: 6 residues within 4Å: Chain A: V.626 Chain B: Y.819, G.823, G.824, L.827 Ligands: PLM.8 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.8: 6 residues within 4Å: Chain B: V.536, Y.819 Chain F: A.93, I.150, V.154 Ligands: PLM.6 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain F Hydrophobic interactions: B:Y.819, B:Y.819, F:I.150, F:V.154 PLM.11: 6 residues within 4Å: Chain B: F.629 Chain C: W.548, I.551, Y.555, F.606 Ligands: OLC.12 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:I.551, C:Y.555, C:F.606, B:F.629 PLM.15: 6 residues within 4Å: Chain C: V.626 Chain D: V.536, Y.819, G.823, G.824 Ligands: PLM.17 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:Y.819, C:V.626 PLM.17: 7 residues within 4Å: Chain D: V.536, Y.819, I.822 Chain H: A.93, I.150, V.154 Ligands: PLM.15 4 PLIP interactions: 2 interactions with chain H, 2 interactions with chain D Hydrophobic interactions: H:I.150, H:V.154, D:Y.819, D:Y.819

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

OLC.3: 8 residues within 4Å: Chain A: F.537, F.596, I.820 Chain D: R.621, G.625, V.626, F.629 Ligands: POV.19 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.7: 7 residues within 4Å: Chain A: R.621, G.625, F.629 Chain B: F.537, F.596, L.603, I.820 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:F.629, A:F.629, B:F.537, B:F.596, B:I.820 OLC.12: 9 residues within 4Å: Chain B: G.625, V.626, F.629 Chain C: F.537, F.596, L.603, I.820 Ligands: PLM.11, POV.20 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:F.596, C:L.603, C:I.820, C:I.820, B:V.626, B:F.629 OLC.16: 7 residues within 4Å: Chain C: R.621, G.625, F.629 Chain D: F.537, F.596, L.603, I.820 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:R.621, C:F.629, C:F.629, D:F.537, D:F.596, D:L.603, D:I.820

4 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.4: 10 residues within 4Å: Chain A: Y.472, P.500, T.502, R.507, L.672, G.675, S.676, T.677, L.726, E.727 9 PLIP interactions: 9 interactions with chain A, Hydrophobic interactions: A:Y.472 Hydrogen bonds: A:T.502, A:R.507, A:R.507, A:S.676, A:T.677, A:T.677, A:E.727, A:E.727 GLU.9: 10 residues within 4Å: Chain B: Y.472, P.500, T.502, R.507, G.675, S.676, T.677, L.726, E.727, Y.754 10 PLIP interactions: 10 interactions with chain B, Hydrophobic interactions: B:Y.472, B:E.727 Hydrogen bonds: B:P.500, B:T.502, B:R.507, B:R.507, B:S.676, B:T.677, B:T.677, B:E.727 GLU.13: 11 residues within 4Å: Chain C: Y.472, P.500, T.502, R.507, L.672, G.675, S.676, T.677, L.726, E.727, Y.754 8 PLIP interactions: 8 interactions with chain C, Hydrophobic interactions: C:Y.472 Hydrogen bonds: C:T.502, C:R.507, C:R.507, C:S.676, C:T.677, C:E.727, C:E.727 GLU.18: 9 residues within 4Å: Chain D: Y.472, P.500, T.502, R.507, G.675, S.676, T.677, L.726, E.727 10 PLIP interactions: 10 interactions with chain D, Hydrophobic interactions: D:Y.472, D:E.727 Hydrogen bonds: D:P.500, D:T.502, D:R.507, D:R.507, D:S.676, D:T.677, D:T.677, D:E.727

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

POV.19: 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: T.92, A.93, L.97, I.150 Ligands: OLC.3 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:Y.819, D:V.626 Hydrogen bonds: E:T.92 POV.20: 15 residues within 4Å: Chain B: I.622, V.626 Chain C: V.536, F.537, Y.819, I.820, G.823, G.824, G.826, L.827 Chain G: T.92, A.93, L.97, I.150 Ligands: OLC.12 8 PLIP interactions: 4 interactions with chain C, 2 interactions with chain G, 2 interactions with chain B Hydrophobic interactions: C:F.537, C:Y.819, C:Y.819, C:L.827, G:I.150, B:I.622, B:V.626 Hydrogen bonds: G:T.92

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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