SMTL ID : 7qhh.1

Desensitized state of GluA1/2 AMPA receptor in complex with TARP-gamma 8 (TMD-LBD)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.60 Å

Oligo State

hetero-2-2-2-mer

Ligands

4 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.1: 12 residues within 4Å: Chain A: Y.472, P.500, L.501, T.502, T.671, L.672, G.675, S.676, T.677, K.678, L.725, M.730 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:T.677 Hydrogen bonds: A:T.502, A:T.671, A:L.672, A:S.676, A:T.677, A:K.678 GLU.5: 9 residues within 4Å: Chain B: Y.471, G.472, P.499, L.500, T.501, L.671, G.674, S.675, T.676 9 PLIP interactions: 7 interactions with chain B, 2 Ligand-Ligand interactions Hydrophobic interactions: B:L.671 Hydrogen bonds: B:G.472, B:P.499, B:T.501, B:S.675, B:T.676, E.5, E.5 Salt bridges: B:K.751 GLU.8: 12 residues within 4Å: Chain C: Y.472, P.500, L.501, T.502, T.671, L.672, G.675, S.676, T.677, K.678, L.725, M.730 7 PLIP interactions: 7 interactions with chain C, Hydrophobic interactions: C:T.677 Hydrogen bonds: C:T.502, C:T.671, C:L.672, C:S.676, C:T.677, C:K.678 GLU.12: 9 residues within 4Å: Chain D: Y.471, G.472, P.499, L.500, T.501, L.671, G.674, S.675, T.676 9 PLIP interactions: 2 Ligand-Ligand interactions, 7 interactions with chain D Hydrogen bonds: E.12, E.12, D:G.472, D:P.499, D:T.501, D:S.675, D:T.676 Hydrophobic interactions: D:L.671 Salt bridges: D:K.751

10 x PAM: PALMITOLEIC ACID(Non-covalent)

PAM.2: 5 residues within 4Å: Chain A: L.811, F.818, Y.819, I.822 Chain B: C.549 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.811, A:F.818, A:F.818 PAM.4: 7 residues within 4Å: Chain A: Y.545, W.548, Y.555, L.603, F.606, M.607 Ligands: OLC.3 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.545, A:W.548, A:Y.555, A:L.603, A:F.606 PAM.7: 5 residues within 4Å: Chain B: F.536, L.539, Y.544, I.819 Ligands: 79N.6 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.536, B:L.539, B:Y.544, B:I.819, B:I.819 Hydrogen bonds: B:Y.544 PAM.9: 5 residues within 4Å: Chain C: L.811, F.818, Y.819, I.822 Chain D: C.549 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.811, C:F.818, C:F.818 PAM.11: 7 residues within 4Å: Chain C: Y.545, W.548, Y.555, L.603, F.606, M.607 Ligands: OLC.10 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:Y.545, C:W.548, C:Y.555, C:L.603, C:F.606 PAM.14: 5 residues within 4Å: Chain D: F.536, L.539, Y.544, I.819 Ligands: 79N.13 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:F.536, D:L.539, D:Y.544, D:I.819, D:I.819 Hydrogen bonds: D:Y.544 PAM.15: 4 residues within 4Å: Chain A: V.626 Chain D: F.536, L.826 Chain E: A.117 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:V.626, D:F.536, D:L.826 PAM.16: 8 residues within 4Å: Chain E: F.32, T.36, I.39, W.87, R.88, K.102, A.135, I.136 7 PLIP interactions: 7 interactions with chain E Hydrophobic interactions: E:F.32, E:T.36, E:I.39, E:W.87, E:A.135, E:I.136 Salt bridges: E:R.88 PAM.17: 4 residues within 4Å: Chain B: F.536, L.826 Chain C: V.626 Chain F: A.117 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:F.536, B:L.826, C:V.626 PAM.18: 8 residues within 4Å: Chain F: F.32, T.36, I.39, W.87, R.88, K.102, A.135, I.136 7 PLIP interactions: 7 interactions with chain F Hydrophobic interactions: F:F.32, F:T.36, F:I.39, F:W.87, F:A.135, F:I.136 Salt bridges: F:R.88

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

OLC.3: 5 residues within 4Å: Chain A: F.537, L.540, L.603, I.820 Ligands: PAM.4 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.537, A:L.540, A:L.603, A:L.603, A:I.820, A:I.820 OLC.10: 5 residues within 4Å: Chain C: F.537, L.540, L.603, I.820 Ligands: PAM.11 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:F.537, C:L.540, C:L.603, C:L.603, C:I.820, C:I.820

2 x 79N: (2S)-2,3-dihydroxypropyl (7Z)-hexadec-7-enoate(Non-covalent)

79N.6: 6 residues within 4Å: Chain B: Y.544, M.548, Y.554, F.605 Chain C: F.629 Ligands: PAM.7 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:F.629, B:Y.554, B:F.605 79N.13: 6 residues within 4Å: Chain A: F.629 Chain D: Y.544, M.548, Y.554, F.605 Ligands: PAM.14 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain D Hydrophobic interactions: A:F.629, D:Y.554, D:F.605

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Herguedas, B. et al., Mechanisms underlying TARP modulation of the GluA1/2-gamma 8 AMPA receptor. Nat Commun (2022)

Release Date

2022-02-23

Peptides

Isoform Flip of Glutamate receptor 1: AC
Isoform Flip of Glutamate receptor 2: BD
Voltage-dependent calcium channel gamma-8 subunit: EF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

E
J

F
I

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

Voltage-dependent calcium channel gamma-8 subunit

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