SMTL ID : 8c1r.1

Resting state homomeric GluA2 F231A mutant AMPA receptor in complex with TARP gamma-2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.20 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: 12 residues within 4Å: Chain A: E.431, Y.434, Y.479, P.507, L.508, T.509, R.514, G.682, S.683, E.734, M.737, Y.761 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.479 Hydrogen bonds: A:P.507, A:T.509, A:T.509, A:R.514, A:R.514, A:S.683, A:S.683 pi-Stacking: A:Y.479 Halogen bonds: A:Y.761 ZK1.5: 13 residues within 4Å: Chain B: Y.434, Y.479, P.507, L.508, T.509, R.514, G.682, S.683, T.715, E.734, T.736, M.737, Y.761 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:P.507 Hydrogen bonds: B:P.507, B:T.509, B:T.509, B:R.514, B:R.514, B:S.683, B:S.683, B:S.683, B:T.715 pi-Stacking: B:Y.479, B:Y.479 Halogen bonds: B:T.736 ZK1.9: 12 residues within 4Å: Chain C: E.431, Y.434, Y.479, P.507, L.508, T.509, R.514, S.683, E.734, T.736, M.737, Y.761 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:Y.479, C:Y.479 Hydrogen bonds: C:P.507, C:T.509, C:T.509, C:R.514, C:R.514, C:S.683, C:S.683, C:S.683 pi-Stacking: C:Y.479 Halogen bonds: C:E.431 ZK1.12: 14 residues within 4Å: Chain D: E.431, Y.434, Y.479, P.507, L.508, T.509, R.514, G.682, S.683, T.715, E.734, T.736, M.737, Y.761 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:P.507, D:T.509, D:R.514, D:R.514, D:S.683, D:S.683, D:S.683, D:T.715 pi-Stacking: D:Y.479, D:Y.479 Halogen bonds: D:E.431

7 x PLM: PALMITIC ACID(Non-covalent)

PLM.2: 6 residues within 4Å: Chain A: L.547, Y.552, W.555, F.613 Ligands: OLC.3, PLM.17 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.547, A:Y.552, A:Y.552, A:W.555, A:W.555, A:F.613 PLM.4: 3 residues within 4Å: Chain A: I.602 Chain F: M.191, V.194 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain A Hydrophobic interactions: F:V.194 Hydrogen bonds: A:I.602 PLM.6: 7 residues within 4Å: Chain B: L.547, Y.552, W.555, Y.562, L.610, F.613 Ligands: OLC.7 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.547, B:Y.552, B:W.555, B:Y.562, B:Y.562, B:L.610, B:F.613, B:F.613 PLM.11: 7 residues within 4Å: Chain C: L.547, Y.552, W.555, I.558, Y.562, F.613 Ligands: OLC.10 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:L.547, C:W.555, C:I.558, C:Y.562, C:F.613 PLM.13: 6 residues within 4Å: Chain D: L.547, Y.552, W.555, Y.562, F.613 Ligands: OLC.14 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:Y.552, D:Y.552, D:W.555, D:Y.562, D:F.613 PLM.17: 5 residues within 4Å: Chain A: Y.552 Chain F: S.174, Y.180 Ligands: PLM.2, OLC.3 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain F Hydrophobic interactions: A:Y.552 Hydrogen bonds: F:Y.180, F:Y.180 PLM.18: 4 residues within 4Å: Chain G: S.174, Y.175, Y.180 Ligands: OLC.7 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:Y.175, G:Y.180, G:Y.180

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

OLC.3: 11 residues within 4Å: Chain A: F.544, F.603, W.607, L.610, I.827 Chain D: G.632, V.633, F.636 Ligands: PLM.2, POV.16, PLM.17 7 PLIP interactions: 3 interactions with chain D, 4 interactions with chain A Hydrophobic interactions: D:V.633, D:F.636, D:F.636, A:F.544, A:F.603, A:W.607, A:I.827 OLC.7: 12 residues within 4Å: Chain A: I.629, G.632, V.633, F.636 Chain B: F.544, F.603, L.610, M.614, I.827 Ligands: PLM.6, POV.8, PLM.18 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.603, B:L.610, B:I.827, A:V.633, A:F.636 OLC.10: 10 residues within 4Å: Chain B: R.628, G.632, F.636 Chain C: F.544, F.603, W.607, L.610, I.827 Ligands: PLM.11, POV.20 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:F.603, C:W.607, C:I.827, B:F.636, B:F.636 OLC.14: 9 residues within 4Å: Chain C: R.628, G.632, F.636 Chain D: F.544, L.547, F.603, L.610 Ligands: PLM.13, POV.15 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:F.544, D:F.603, D:L.610, C:F.636

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

POV.8: 14 residues within 4Å: Chain A: V.633 Chain B: V.543, F.544, Y.826, I.827, G.830, G.831, L.834 Chain F: A.93, F.96, F.106, I.150, V.154 Ligands: OLC.7 7 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A, 2 interactions with chain F Hydrophobic interactions: B:F.544, B:Y.826, B:I.827, B:L.834, A:V.633, F:F.106, F:I.150 POV.15: 12 residues within 4Å: Chain D: V.543, F.544, Y.826, I.827, G.830, G.831, L.834 Chain H: A.93, F.96, F.106, I.150 Ligands: OLC.14 7 PLIP interactions: 5 interactions with chain H, 2 interactions with chain D Hydrophobic interactions: H:F.96, H:F.106, H:F.106, H:I.150, H:I.150, D:Y.826, D:L.834 POV.16: 10 residues within 4Å: Chain A: G.542, V.543, F.544, Y.826, G.831, L.834 Chain E: A.93, F.96, L.97 Ligands: OLC.3 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.544, A:L.834 POV.19: 6 residues within 4Å: Chain B: I.563, I.602, F.603 Chain G: V.194, L.195, H.198 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain G Hydrophobic interactions: B:I.563, B:I.602, B:F.603, B:F.603, G:L.195 Salt bridges: G:H.198 POV.20: 14 residues within 4Å: Chain B: V.633 Chain C: G.542, V.543, F.544, Y.826, I.827, G.830, G.831 Chain G: D.91, A.93, F.96, L.97, I.150 Ligands: OLC.10 6 PLIP interactions: 4 interactions with chain G, 1 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: G:L.97, G:I.150, G:I.150, B:V.633, C:Y.826 Salt bridges: G:D.91

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 2: ABCD
Voltage-dependent calcium channel gamma-2 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 2

Voltage-dependent calcium channel gamma-2 subunit

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