SMTL ID : 7lep.1

The composite LBD-TMD structure combined from all hippocampal AMPAR subtypes at 3.25 Angstrom resolution

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-2-1-2-2-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)(Covalent)

ZK1.1: 10 residues within 4Å: Chain A: Y.12, Y.57, P.85, L.86, T.87, R.92, G.250, S.251, T.283, E.302 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.57 Hydrogen bonds: A:P.85, A:T.87, A:T.87, A:R.92, A:R.92, A:S.251 ZK1.10: 11 residues within 4Å: Chain B: E.7, Y.55, P.83, L.84, T.85, R.90, G.258, S.259, E.310, M.313, Y.337 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:P.83, B:T.85, B:R.90, B:R.90, B:S.259, B:E.310 pi-Stacking: B:Y.55 Halogen bonds: B:Y.337 ZK1.17: 11 residues within 4Å: Chain C: D.10, Y.12, Y.57, P.85, L.86, T.87, R.92, G.249, S.250, T.282, E.301 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:Y.57 Hydrogen bonds: C:P.85, C:T.87, C:T.87, C:R.92, C:S.250 Halogen bonds: C:D.10 ZK1.26: 10 residues within 4Å: Chain D: E.7, Y.55, P.83, T.85, R.90, G.258, S.259, E.310, M.313, Y.337 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:Y.55 Hydrogen bonds: D:P.83, D:T.85, D:R.90, D:R.90, D:S.259, D:E.310 pi-Stacking: D:Y.55 Halogen bonds: D:Y.337

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

POV.2: 1 residues within 4Å: Chain A: E.410 Ligand excluded by PLIP POV.3: 2 residues within 4Å: Chain A: Y.140 Ligands: POV.6 Ligand excluded by PLIP POV.4: 4 residues within 4Å: Chain A: F.122, I.395 Ligands: POV.5, POV.6 Ligand excluded by PLIP POV.5: 5 residues within 4Å: Chain A: F.171, W.175, L.178 Ligands: POV.4, POV.7 Ligand excluded by PLIP POV.6: 5 residues within 4Å: Chain A: W.133, V.137, F.181 Ligands: POV.3, POV.4 Ligand excluded by PLIP POV.7: 2 residues within 4Å: Chain A: L.402 Ligands: POV.5 Ligand excluded by PLIP POV.8: 3 residues within 4Å: Chain A: I.170, F.171 Ligands: POV.9 Ligand excluded by PLIP POV.9: 2 residues within 4Å: Chain A: F.171 Ligands: POV.8 Ligand excluded by PLIP POV.11: 10 residues within 4Å: Chain B: G.118, V.119, F.120, Y.402, G.407 Chain G: L.102, L.103, F.112, V.160 Ligands: POV.14 Ligand excluded by PLIP POV.13: 3 residues within 4Å: Chain B: F.146, I.178 Chain F: S.72 Ligand excluded by PLIP POV.14: 3 residues within 4Å: Chain B: F.179, L.186 Ligands: POV.11 Ligand excluded by PLIP POV.15: 4 residues within 4Å: Chain B: Y.128, W.131, V.135 Ligands: C14.12 Ligand excluded by PLIP POV.16: 3 residues within 4Å: Chain B: L.413, I.417, E.418 Ligand excluded by PLIP POV.19: 2 residues within 4Å: Chain C: M.134, Y.140 Ligand excluded by PLIP POV.20: 1 residues within 4Å: Chain C: E.409 Ligand excluded by PLIP POV.21: 3 residues within 4Å: Chain C: I.169, F.170 Ligands: POV.22 Ligand excluded by PLIP POV.22: 2 residues within 4Å: Chain C: F.170 Ligands: POV.21 Ligand excluded by PLIP POV.23: 1 residues within 4Å: Chain C: L.401 Ligand excluded by PLIP POV.24: 6 residues within 4Å: Chain C: F.122, L.125, M.181, I.394 Ligands: D10.18, POV.25 Ligand excluded by PLIP POV.25: 5 residues within 4Å: Chain B: L.201 Chain C: F.170, W.174, L.177 Ligands: POV.24 Ligand excluded by PLIP POV.27: 10 residues within 4Å: Chain D: G.118, V.119, F.120, Y.402, G.407 Chain H: L.102, L.103, F.112, V.160 Ligands: POV.31 Ligand excluded by PLIP POV.28: 3 residues within 4Å: Chain D: F.146, I.178 Chain E: S.72 Ligand excluded by PLIP POV.29: 4 residues within 4Å: Chain D: Y.128, W.131, M.132, V.135 Ligand excluded by PLIP POV.30: 2 residues within 4Å: Chain D: I.403 Ligands: POV.31 Ligand excluded by PLIP POV.31: 3 residues within 4Å: Chain D: F.179 Ligands: POV.27, POV.30 Ligand excluded by PLIP POV.32: 3 residues within 4Å: Chain D: L.413, I.417, E.418 Ligand excluded by PLIP POV.33: 2 residues within 4Å: Chain E: G.75, L.79 Ligand excluded by PLIP POV.34: 2 residues within 4Å: Chain F: G.75, L.79 Ligand excluded by PLIP POV.38: 3 residues within 4Å: Chain G: G.142, I.145, L.146 Ligand excluded by PLIP POV.42: 4 residues within 4Å: Chain H: L.119, G.142, I.145, L.146 Ligand excluded by PLIP

1 x C14: TETRADECANE(Non-covalent)

C14.12: 5 residues within 4Å: Chain A: G.200, F.204 Chain B: F.120, I.403 Ligands: POV.15 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:I.403, A:F.204

1 x D10: DECANE(Non-covalent)

D10.18: 3 residues within 4Å: Chain C: Y.130, W.133 Ligands: POV.24 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Y.130, C:W.133

2 x XVD: 6-[2-chloro-6-(trifluoromethoxy)phenyl]-1H-benzimidazol-2-ol(Non-covalent)

XVD.35: 13 residues within 4Å: Chain A: Y.130, E.131, M.134, C.135, F.138 Chain G: M.17, N.154, V.158, I.162, F.187, Y.188, G.190, G.191 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain G Hydrophobic interactions: A:F.138, A:F.138, G:F.187, G:Y.188 Hydrogen bonds: G:N.154, G:N.154, G:F.187 XVD.39: 13 residues within 4Å: Chain C: Y.130, E.131, M.134, C.135, F.138 Chain H: M.17, N.154, V.158, I.162, F.187, Y.188, G.190, G.191 8 PLIP interactions: 3 interactions with chain C, 5 interactions with chain H Hydrophobic interactions: C:M.134, C:F.138, C:F.138, H:F.187, H:Y.188 Hydrogen bonds: H:N.154, H:N.154, H:F.187

2 x OCT: N-OCTANE(Non-covalent)

OCT.36: 3 residues within 4Å: Chain A: V.145 Chain G: V.202, L.203 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain G Hydrophobic interactions: A:V.145, G:V.202, G:L.203 OCT.40: 3 residues within 4Å: Chain C: V.145 Chain H: V.202, L.203 3 PLIP interactions: 2 interactions with chain H, 1 interactions with chain C Hydrophobic interactions: H:V.202, H:L.203, C:V.145

2 x D12: DODECANE(Non-covalent)

D12.37: 2 residues within 4Å: Chain G: T.18, I.21 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:I.21 D12.41: 2 residues within 4Å: Chain H: T.18, I.21 1 PLIP interactions: 1 interactions with chain H Hydrophobic interactions: H:I.21

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yu, J. et al., Hippocampal AMPA receptor assemblies and mechanism of allosteric inhibition. Nature (2021)

Release Date

2021-05-12

Peptides

Mix of AMPAR subunits (GluA1, GluA3, and GluA4): A
Glutamate receptor 2: BD
Mix of AMPAR subunits (GluA1, GluA3, and GluAX): C
Protein cornichon homolog 2: EF
Voltage-dependent calcium channel gamma-8 subunit: GH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D
D

C
C

E
E

F
F

G
G

H
H

Membrane

We predict this structure to be a membrane protein.
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Mix of AMPAR subunits (GluA1, GluA3, and GluA4)

Glutamate receptor 2

Mix of AMPAR subunits (GluA1, GluA3, and GluAX)

Protein cornichon homolog 2

Voltage-dependent calcium channel gamma-8 subunit