SMTL ID : 7ocf.1

Active state GluA1/A2 AMPA receptor in complex with TARP gamma 8 and CNIH2 (LBD-TMD)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-2-mer

Ligands

4 x CYZ: CYCLOTHIAZIDE(Non-covalent)

CYZ.1: 9 residues within 4Å: Chain A: P.516, M.518, S.519, L.773, S.776, L.781, K.785 Chain B: S.750, K.751 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.773, A:L.781 Hydrogen bonds: A:S.776, A:S.776, B:S.750 CYZ.9: 12 residues within 4Å: Chain A: I.503, S.751, K.752, G.753 Chain B: K.514, P.515, M.517, S.518, S.775, L.780, D.781, K.784 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:K.514 Hydrogen bonds: B:S.518, B:S.775, B:S.775, A:S.751 CYZ.18: 9 residues within 4Å: Chain E: P.516, M.518, S.519, L.773, S.776, L.781, K.785 Chain H: S.750, K.751 5 PLIP interactions: 4 interactions with chain E, 1 interactions with chain H Hydrophobic interactions: E:L.773, E:L.781 Hydrogen bonds: E:S.776, E:S.776, H:S.750 CYZ.29: 12 residues within 4Å: Chain E: I.503, S.751, K.752, G.753 Chain H: K.514, P.515, M.517, S.518, S.775, L.780, D.781, K.784 5 PLIP interactions: 4 interactions with chain H, 1 interactions with chain E Hydrophobic interactions: H:K.514 Hydrogen bonds: H:S.518, H:S.775, H:S.775, E:S.751

26 x PC1: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PC1.2: 6 residues within 4Å: Chain A: L.540, Y.545, W.548, L.603, F.606 Ligands: PC1.7 Ligand excluded by PLIP PC1.3: 4 residues within 4Å: Chain A: G.824 Ligands: PC1.4, PC1.6, PC1.7 Ligand excluded by PLIP PC1.4: 5 residues within 4Å: Chain A: I.834, Y.838 Ligands: PC1.3, PC1.5, PC1.7 Ligand excluded by PLIP PC1.5: 3 residues within 4Å: Chain A: F.596 Ligands: PC1.4, PC1.27 Ligand excluded by PLIP PC1.6: 6 residues within 4Å: Chain A: G.826 Chain C: L.14, V.15, A.18, F.22 Ligands: PC1.3 Ligand excluded by PLIP PC1.7: 6 residues within 4Å: Chain A: F.537, F.596 Chain B: I.621 Ligands: PC1.2, PC1.3, PC1.4 Ligand excluded by PLIP PC1.10: 7 residues within 4Å: Chain B: L.539, Y.544, W.547, M.548, V.551, Y.554 Ligands: PC1.14 Ligand excluded by PLIP PC1.11: 6 residues within 4Å: Chain B: Y.818, V.821, G.825, L.832 Chain D: V.178 Ligands: PC1.16 Ligand excluded by PLIP PC1.12: 2 residues within 4Å: Chain B: F.595 Ligands: PC1.13 Ligand excluded by PLIP PC1.13: 7 residues within 4Å: Chain B: V.559, F.562, G.593 Chain C: V.69, S.73, L.77 Ligands: PC1.12 Ligand excluded by PLIP PC1.14: 9 residues within 4Å: Chain B: F.536, L.539, Y.544, F.595, L.598 Chain E: I.622, F.629 Ligands: PC1.10, PC1.16 Ligand excluded by PLIP PC1.16: 4 residues within 4Å: Chain B: V.535 Chain D: A.117 Ligands: PC1.11, PC1.14 Ligand excluded by PLIP PC1.17: 3 residues within 4Å: Chain D: V.217, N.224 Ligands: PC1.22 Ligand excluded by PLIP PC1.19: 6 residues within 4Å: Chain E: L.540, Y.545, W.548, L.603, F.606 Ligands: PC1.24 Ligand excluded by PLIP PC1.20: 4 residues within 4Å: Chain E: G.824 Ligands: PC1.21, PC1.23, PC1.24 Ligand excluded by PLIP PC1.21: 4 residues within 4Å: Chain E: I.834 Ligands: PC1.20, PC1.22, PC1.24 Ligand excluded by PLIP PC1.22: 3 residues within 4Å: Chain E: F.596 Ligands: PC1.17, PC1.21 Ligand excluded by PLIP PC1.23: 7 residues within 4Å: Chain E: G.826 Chain F: L.14, V.15, A.18, F.22, L.157 Ligands: PC1.20 Ligand excluded by PLIP PC1.24: 6 residues within 4Å: Chain E: F.537, F.596 Chain H: I.621 Ligands: PC1.19, PC1.20, PC1.21 Ligand excluded by PLIP PC1.26: 8 residues within 4Å: Chain F: V.69, P.70, S.73, L.77 Chain H: V.559, F.562, G.593 Ligands: PC1.32 Ligand excluded by PLIP PC1.27: 3 residues within 4Å: Chain G: V.217, N.224 Ligands: PC1.5 Ligand excluded by PLIP PC1.28: 4 residues within 4Å: Chain G: A.117 Chain H: V.535 Ligands: PC1.31, PC1.33 Ligand excluded by PLIP PC1.30: 7 residues within 4Å: Chain H: L.539, Y.544, W.547, M.548, V.551, Y.554 Ligands: PC1.33 Ligand excluded by PLIP PC1.31: 8 residues within 4Å: Chain G: A.167, I.174, V.178 Chain H: Y.818, V.821, G.825, L.832 Ligands: PC1.28 Ligand excluded by PLIP PC1.32: 2 residues within 4Å: Chain H: F.595 Ligands: PC1.26 Ligand excluded by PLIP PC1.33: 9 residues within 4Å: Chain A: I.622, F.629 Chain H: F.536, L.539, Y.544, F.595, L.598 Ligands: PC1.28, PC1.30 Ligand excluded by PLIP

4 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.8: 9 residues within 4Å: Chain A: Y.472, T.502, R.507, G.675, S.676, T.677, L.726, E.727, M.730 9 PLIP interactions: 5 interactions with chain A, 4 Ligand-Ligand interactions Hydrophobic interactions: A:Y.472, A:T.677 Hydrogen bonds: A:R.507, A:S.676, A:E.727, E.8, E.8, E.8, E.8 GLU.15: 10 residues within 4Å: Chain B: Y.471, P.499, L.500, T.501, R.506, L.671, G.674, S.675, T.676, E.726 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:Y.471 Hydrogen bonds: B:P.499, B:T.501, B:R.506, B:S.675 GLU.25: 9 residues within 4Å: Chain E: Y.472, T.502, R.507, G.675, S.676, T.677, L.726, E.727, M.730 9 PLIP interactions: 5 interactions with chain E, 4 Ligand-Ligand interactions Hydrophobic interactions: E:Y.472, E:T.677 Hydrogen bonds: E:R.507, E:S.676, E:E.727, E.25, E.25, E.25, E.25 GLU.34: 10 residues within 4Å: Chain H: Y.471, P.499, L.500, T.501, R.506, L.671, G.674, S.675, T.676, E.726 5 PLIP interactions: 5 interactions with chain H, Hydrophobic interactions: H:Y.471 Hydrogen bonds: H:P.499, H:T.501, H:R.506, H:S.675

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, D. et al., Gating and modulation of a hetero-octameric AMPA glutamate receptor. Nature (2021)

Release Date

2021-06-09

Peptides

Isoform Flip of Glutamate receptor 1: AE
Isoform Flip of Glutamate receptor 2: BH
Protein cornichon homolog 2: CF
Voltage-dependent calcium channel gamma-8 subunit: DG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
C

B
B

H
D

C
G

F
E

D
I

G
J

Membrane

We predict this structure to be a membrane protein.
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Isoform Flip of Glutamate receptor 1

Isoform Flip of Glutamate receptor 2

Protein cornichon homolog 2

Voltage-dependent calcium channel gamma-8 subunit

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