SMTL ID : 7qhb.1

Active state of GluA1/2 in complex with TARP gamma 8, L-glutamate and CTZ

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-mer

Ligands

14 x PAM: PALMITOLEIC ACID(Non-covalent)

PAM.1: 4 residues within 4Å: Chain A: L.811, Y.819, I.822 Chain B: C.549 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.819, A:I.822 PAM.5: 3 residues within 4Å: Chain A: W.548, M.549 Ligands: OLC.4 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.548 PAM.11: 7 residues within 4Å: Chain B: V.535, F.536, L.539, Y.544 Chain E: A.117 Ligands: 79N.9, 79N.10 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.536, B:L.539, B:Y.544 PAM.12: 4 residues within 4Å: Chain C: L.811, Y.819, I.822 Chain D: C.549 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Y.819, C:I.822 PAM.16: 3 residues within 4Å: Chain C: W.548, M.549 Ligands: OLC.15 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:W.548 PAM.20: 7 residues within 4Å: Chain D: V.535, F.536, L.539, Y.544 Chain F: A.117 Ligands: 79N.6, 79N.19 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:F.536, D:L.539, D:Y.544 PAM.21: 3 residues within 4Å: Chain B: F.536 Chain E: A.117 Ligands: PAM.24 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain B Hydrophobic interactions: E:A.117, B:F.536 PAM.22: 4 residues within 4Å: Chain C: I.595, F.596 Chain E: V.220, N.224 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain E Hydrophobic interactions: C:I.595, C:F.596, E:V.220 PAM.23: 1 residues within 4Å: Chain E: W.87 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:W.87 Hydrogen bonds: E:R.88 PAM.24: 5 residues within 4Å: Chain B: L.826 Chain E: A.117, L.121, I.174 Ligands: PAM.21 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain E Hydrogen bonds: B:Y.818 Hydrophobic interactions: E:I.174 PAM.25: 4 residues within 4Å: Chain A: I.595, F.596 Chain F: V.220, N.224 3 PLIP interactions: 1 interactions with chain F, 2 interactions with chain A Hydrophobic interactions: F:V.220, A:I.595, A:F.596 PAM.26: 3 residues within 4Å: Chain D: F.536 Chain F: A.117 Ligands: PAM.28 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain F Hydrophobic interactions: D:F.536, F:A.117 PAM.27: 1 residues within 4Å: Chain F: W.87 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:W.87 Hydrogen bonds: F:R.88 PAM.28: 6 residues within 4Å: Chain D: Y.818, L.826 Chain F: A.117, L.121, I.174 Ligands: PAM.26 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain F Hydrogen bonds: D:Y.818 Hydrophobic interactions: F:I.174

4 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.2: 9 residues within 4Å: Chain A: Y.472, P.500, L.501, T.502, R.507, G.675, S.676, T.677, E.727 12 PLIP interactions: 8 interactions with chain A, 4 Ligand-Ligand interactions Hydrophobic interactions: A:Y.472, A:Y.472 Hydrogen bonds: A:T.502, A:T.502, A:S.676, A:T.677, A:T.677, E.2, E.2, E.2, E.2 Salt bridges: A:R.507 GLU.7: 9 residues within 4Å: Chain B: Y.471, P.499, L.500, T.501, R.506, G.674, S.675, T.676, E.726 9 PLIP interactions: 7 interactions with chain B, 2 Ligand-Ligand interactions Hydrophobic interactions: B:Y.471, B:E.726 Hydrogen bonds: B:T.501, B:T.501, B:S.675, B:T.676, E.7, E.7 Salt bridges: B:R.506 GLU.13: 9 residues within 4Å: Chain C: Y.472, P.500, L.501, T.502, R.507, G.675, S.676, T.677, E.727 12 PLIP interactions: 4 Ligand-Ligand interactions, 8 interactions with chain C Hydrogen bonds: E.13, E.13, E.13, E.13, C:T.502, C:T.502, C:S.676, C:T.677, C:T.677 Hydrophobic interactions: C:Y.472, C:Y.472 Salt bridges: C:R.507 GLU.17: 9 residues within 4Å: Chain D: Y.471, P.499, L.500, T.501, R.506, G.674, S.675, T.676, E.726 9 PLIP interactions: 7 interactions with chain D, 2 Ligand-Ligand interactions Hydrophobic interactions: D:Y.471, D:E.726 Hydrogen bonds: D:T.501, D:T.501, D:S.675, D:T.676, E.17, E.17 Salt bridges: D:R.506

4 x CYZ: CYCLOTHIAZIDE(Non-covalent)

CYZ.3: 14 residues within 4Å: Chain A: K.515, P.516, F.517, M.518, S.519, L.773, L.781, D.782, K.785 Chain B: I.502, S.518, S.750, K.751, G.752 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:K.515, A:P.516, A:L.773, A:L.781, B:I.502, B:I.502 Hydrogen bonds: A:S.519, A:D.782 CYZ.8: 14 residues within 4Å: Chain A: I.503, S.519, S.751, K.752, G.753 Chain B: K.514, P.515, F.516, M.517, S.518, S.775, L.780, D.781, K.784 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:I.503, A:K.752, B:K.514 Hydrogen bonds: A:S.751, A:S.751, B:S.518, B:S.775, B:S.775 CYZ.14: 14 residues within 4Å: Chain C: K.515, P.516, F.517, M.518, S.519, L.773, L.781, D.782, K.785 Chain D: I.502, S.518, S.750, K.751, G.752 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:K.515, C:P.516, C:L.773, C:L.781, D:I.502, D:I.502 Hydrogen bonds: C:S.519, C:D.782 CYZ.18: 14 residues within 4Å: Chain C: I.503, S.519, S.751, K.752, G.753 Chain D: K.514, P.515, F.516, M.517, S.518, S.775, L.780, D.781, K.784 8 PLIP interactions: 4 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:I.503, C:K.752, D:K.514 Hydrogen bonds: C:S.751, C:S.751, D:S.518, D:S.775, D:S.775

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

OLC.4: 3 residues within 4Å: Chain A: F.537, I.820 Ligands: PAM.5 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.537, A:I.820 OLC.15: 3 residues within 4Å: Chain C: F.537, I.820 Ligands: PAM.16 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.537, C:I.820

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

79N.6: 8 residues within 4Å: Chain A: L.618, R.621, I.622, G.625, F.629 Chain D: F.595, L.602 Ligands: PAM.20 6 PLIP interactions: 2 interactions with chain D, 4 interactions with chain A Hydrophobic interactions: D:F.595, D:L.602, A:L.618, A:F.629, A:F.629 Salt bridges: A:R.621 79N.9: 5 residues within 4Å: Chain B: L.539, Y.544, W.547, L.602 Ligands: PAM.11 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.539, B:W.547, B:W.547, B:L.602 79N.10: 8 residues within 4Å: Chain B: F.595, L.602 Chain C: L.618, R.621, I.622, G.625, F.629 Ligands: PAM.11 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:F.595, B:L.602, C:L.618, C:F.629, C:F.629 Salt bridges: C:R.621 79N.19: 5 residues within 4Å: Chain D: L.539, Y.544, W.547, L.602 Ligands: PAM.20 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:L.539, D:W.547, D:W.547, D:L.602

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
I

F
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

Voltage-dependent calcium channel gamma-8 subunit

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