SMTL ID : 8piv.1

Homomeric GluA2 flip R/G-unedited Q/R-edited F231A mutant in tandem with TARP gamma-2, desensitized conformation 1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.46 Å

Oligo State

hetero-4-4-mer

Ligands

7 x PLM: PALMITIC ACID(Non-covalent)

PLM.1: 6 residues within 4Å: Chain A: L.539, Y.544, W.547, F.605 Ligands: OLC.2, PLM.13 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.539, A:Y.544, A:Y.544, A:W.547, A:W.547, A:F.605 PLM.3: 3 residues within 4Å: Chain A: I.594 Chain F: M.192, V.195 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.594 PLM.4: 7 residues within 4Å: Chain B: L.539, Y.544, W.547, Y.554, L.602, F.605 Ligands: OLC.5 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.539, B:Y.544, B:W.547, B:Y.554, B:Y.554, B:L.602, B:F.605, B:F.605 PLM.8: 7 residues within 4Å: Chain C: L.539, Y.544, W.547, I.550, Y.554, F.605 Ligands: OLC.7 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:L.539, C:W.547, C:I.550, C:Y.554, C:F.605 PLM.9: 6 residues within 4Å: Chain D: L.539, Y.544, W.547, Y.554, F.605 Ligands: OLC.10 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:Y.544, D:W.547, D:Y.554, D:F.605 PLM.13: 5 residues within 4Å: Chain A: Y.544 Chain F: S.175, Y.181 Ligands: PLM.1, OLC.2 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain F Hydrophobic interactions: A:Y.544 Hydrogen bonds: F:Y.181, F:Y.181 PLM.14: 4 residues within 4Å: Chain G: S.175, Y.176, Y.181 Ligands: OLC.5 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:Y.176, G:Y.181, G:Y.181

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

OLC.2: 11 residues within 4Å: Chain A: F.536, F.595, W.599, L.602, I.819 Chain D: G.624, V.625, F.628 Ligands: PLM.1, POV.12, PLM.13 5 PLIP interactions: 1 interactions with chain D, 4 interactions with chain A Hydrophobic interactions: D:F.628, A:F.536, A:F.595, A:W.599, A:I.819 OLC.5: 12 residues within 4Å: Chain A: G.624, V.625, F.628 Chain B: F.536, L.539, F.595, L.602, M.606, I.819 Ligands: PLM.4, POV.6, PLM.14 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.595, B:L.602, B:I.819, A:V.625, A:F.628 OLC.7: 10 residues within 4Å: Chain B: R.620, G.624, F.628 Chain C: F.536, F.595, W.599, L.602, I.819 Ligands: PLM.8, POV.16 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:F.595, C:W.599, C:L.602, C:I.819, B:F.628, B:F.628 OLC.10: 9 residues within 4Å: Chain C: R.620, G.624, F.628 Chain D: F.536, L.539, F.595, L.602 Ligands: PLM.9, POV.11 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:F.536, D:F.595, D:L.602, C:F.628

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

POV.6: 14 residues within 4Å: Chain A: V.625 Chain B: V.535, F.536, Y.818, I.819, G.822, G.823, L.826 Chain F: A.94, F.97, F.107, I.151, V.155 Ligands: OLC.5 6 PLIP interactions: 2 interactions with chain F, 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: F:F.107, F:I.151, B:F.536, B:Y.818, B:L.826, A:V.625 POV.11: 12 residues within 4Å: Chain D: V.535, F.536, Y.818, I.819, G.822, G.823, L.826 Chain H: A.94, F.97, F.107, I.151 Ligands: OLC.10 7 PLIP interactions: 5 interactions with chain H, 2 interactions with chain D Hydrophobic interactions: H:F.97, H:F.107, H:F.107, H:I.151, H:I.151, D:Y.818, D:L.826 POV.12: 10 residues within 4Å: Chain A: G.534, V.535, F.536, Y.818, G.823, L.826 Chain E: A.94, F.97, L.98 Ligands: OLC.2 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.536, A:L.826 POV.15: 6 residues within 4Å: Chain B: I.555, I.594, F.595 Chain G: V.195, L.196, H.199 6 PLIP interactions: 2 interactions with chain G, 4 interactions with chain B Hydrophobic interactions: G:L.196, B:I.555, B:I.594, B:F.595, B:F.595 Salt bridges: G:H.199 POV.16: 15 residues within 4Å: Chain B: V.625 Chain C: G.534, V.535, F.536, Y.818, I.819, G.822, G.823 Chain G: D.92, A.94, F.97, L.98, F.107, I.151 Ligands: OLC.7 6 PLIP interactions: 1 interactions with chain C, 4 interactions with chain G, 1 interactions with chain B Hydrophobic interactions: C:Y.818, G:L.98, G:F.107, G:I.151, G:I.151, B:V.625

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: 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

Voltage-dependent calcium channel gamma-2 subunit

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