SMTL ID : 7oca.1

Resting state full-length GluA1/A2 heterotertramer in complex with TARP gamma 8 and CNIH2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-2-2-mer

Ligands

2 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 5 residues within 4Å: Chain A: N.71, S.73, D.74, R.100 Chain E: H.122 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.100, A:R.100 NAG-NAG-BMA.5: 5 residues within 4Å: Chain B: H.122 Chain G: N.71, S.73, D.74, R.100 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:R.100, G:R.100

4 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 5 residues within 4Å: Chain A: R.353, E.355, N.360, Q.362, N.371 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain B: R.206, G.232, H.234, N.256 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain E: R.206, G.232, H.234, N.256 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 5 residues within 4Å: Chain G: R.353, E.355, N.360, Q.362, N.371 No protein-ligand interaction detected (PLIP)

4 x E2Q: 6-nitro-2,3-bis(oxidanylidene)-1,4-dihydrobenzo[f]quinoxaline-7-sulfonamide(Non-covalent)

E2Q.7: 9 residues within 4Å: Chain A: Y.472, P.500, T.502, R.507, S.676, T.708, E.727, M.730, Y.754 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:P.500 Hydrogen bonds: A:T.502, A:T.502, A:R.507, A:R.507, A:S.676, A:T.708, A:T.708 pi-Stacking: A:Y.472 E2Q.17: 8 residues within 4Å: Chain B: Y.471, P.499, T.501, R.506, S.675, T.707, M.729, Y.753 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:Y.471, B:P.499 Hydrogen bonds: B:T.501, B:T.501, B:T.501, B:R.506, B:R.506, B:T.707 E2Q.36: 9 residues within 4Å: Chain E: Y.471, P.499, T.501, R.506, S.675, T.707, E.726, M.729, Y.753 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:Y.471, E:P.499 Hydrogen bonds: E:T.501, E:T.501, E:T.501, E:R.506, E:R.506, E:T.707 E2Q.53: 9 residues within 4Å: Chain G: Y.472, P.500, T.502, R.507, S.676, T.708, E.727, M.730, Y.754 9 PLIP interactions: 9 interactions with chain G Hydrophobic interactions: G:P.500 Hydrogen bonds: G:T.502, G:T.502, G:R.507, G:R.507, G:S.676, G:T.708, G:T.708 pi-Stacking: G:Y.472

6 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.8: 1 residues within 4Å: Chain A: N.257 No protein-ligand interaction detected (PLIP) NAG.9: 5 residues within 4Å: Chain A: N.265, T.267, D.268, H.375, K.386 No protein-ligand interaction detected (PLIP) NAG.18: 3 residues within 4Å: Chain B: N.359, K.361, N.370 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.359, B:N.370 NAG.37: 3 residues within 4Å: Chain E: N.359, K.361, N.370 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.359, E:N.370 NAG.54: 1 residues within 4Å: Chain G: N.257 No protein-ligand interaction detected (PLIP) NAG.55: 5 residues within 4Å: Chain G: N.265, T.267, D.268, H.375, K.386 No protein-ligand interaction detected (PLIP)

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

PC1.10: 8 residues within 4Å: Chain A: F.537, F.596, I.820 Chain B: I.621 Ligands: PC1.11, PC1.13, PC1.16, PC1.47 Ligand excluded by PLIP PC1.11: 8 residues within 4Å: Chain A: L.540, Y.545, W.548, I.551, Y.555 Chain B: F.628 Ligands: PC1.10, PC1.47 Ligand excluded by PLIP PC1.12: 4 residues within 4Å: Chain A: V.536, G.823, G.824 Ligands: PC1.13 Ligand excluded by PLIP PC1.13: 7 residues within 4Å: Chain A: L.827, I.834, E.835, Y.838 Ligands: PC1.10, PC1.12, PC1.16 Ligand excluded by PLIP PC1.14: 7 residues within 4Å: Chain A: I.822, G.823 Chain B: F.567 Chain C: V.15, A.18, M.153 Ligands: PC1.27 Ligand excluded by PLIP PC1.15: 6 residues within 4Å: Chain A: R.616 Chain E: F.595, E.834 Ligands: PC1.39, PC1.42, PC1.44 Ligand excluded by PLIP PC1.16: 6 residues within 4Å: Chain A: Y.555, F.596 Chain B: Y.570 Ligands: PC1.10, PC1.13, PC1.48 Ligand excluded by PLIP PC1.19: 10 residues within 4Å: Chain B: L.539, Y.544, W.547, M.548, Y.554, L.602, F.605, M.606 Ligands: PC1.20, PC1.25 Ligand excluded by PLIP PC1.20: 5 residues within 4Å: Chain B: Y.554, I.555 Ligands: PC1.19, PC1.25, PC1.52 Ligand excluded by PLIP PC1.21: 5 residues within 4Å: Chain B: V.535, G.823 Chain D: A.117 Ligands: PC1.22, PC1.25 Ligand excluded by PLIP PC1.22: 4 residues within 4Å: Chain B: Y.818, G.825 Chain D: A.167 Ligands: PC1.21 Ligand excluded by PLIP PC1.23: 4 residues within 4Å: Chain B: I.833, E.834, Y.837 Ligands: PC1.52 Ligand excluded by PLIP PC1.24: 6 residues within 4Å: Chain B: F.835, C.836 Chain D: N.156, I.163, L.164, A.167 Ligand excluded by PLIP PC1.25: 12 residues within 4Å: Chain B: F.536, Y.544, F.595, L.598, W.599, L.602, I.819 Chain G: F.629 Ligands: PC1.19, PC1.20, PC1.21, PC1.52 Ligand excluded by PLIP PC1.26: 10 residues within 4Å: Chain B: V.559, F.562, R.566, I.594 Chain C: V.69, P.70, S.73, G.76, L.77 Ligands: PC1.30 Ligand excluded by PLIP PC1.27: 8 residues within 4Å: Chain A: F.836 Chain C: A.18, I.21, F.22, I.25, W.26, I.29 Ligands: PC1.14 Ligand excluded by PLIP PC1.28: 2 residues within 4Å: Chain C: L.83, W.88 Ligand excluded by PLIP PC1.30: 2 residues within 4Å: Chain C: W.88 Ligands: PC1.26 Ligand excluded by PLIP PC1.31: 5 residues within 4Å: Chain D: L.137, L.140, C.144, N.156, I.157 Ligand excluded by PLIP PC1.32: 6 residues within 4Å: Chain D: S.200, Y.201, Y.206 Chain G: Y.545 Ligands: PC1.56, PC1.57 Ligand excluded by PLIP PC1.33: 5 residues within 4Å: Chain D: I.213, V.217, V.220, N.224 Ligands: PC1.45 Ligand excluded by PLIP PC1.34: 4 residues within 4Å: Chain D: Y.46, W.203, Y.206, F.207 Ligand excluded by PLIP PC1.35: 4 residues within 4Å: Chain D: E.16, V.19, Q.20, L.214 Ligand excluded by PLIP PC1.38: 10 residues within 4Å: Chain E: L.539, Y.544, W.547, M.548, Y.554, L.602, F.605, M.606 Ligands: PC1.39, PC1.44 Ligand excluded by PLIP PC1.39: 5 residues within 4Å: Chain E: Y.554, I.555 Ligands: PC1.15, PC1.38, PC1.44 Ligand excluded by PLIP PC1.40: 5 residues within 4Å: Chain E: V.535, G.823 Chain F: A.117 Ligands: PC1.41, PC1.44 Ligand excluded by PLIP PC1.41: 3 residues within 4Å: Chain E: Y.818, G.825 Ligands: PC1.40 Ligand excluded by PLIP PC1.42: 4 residues within 4Å: Chain E: I.833, E.834, Y.837 Ligands: PC1.15 Ligand excluded by PLIP PC1.43: 5 residues within 4Å: Chain E: F.835, C.836 Chain F: I.163, L.164, A.167 Ligand excluded by PLIP PC1.44: 12 residues within 4Å: Chain A: F.629 Chain E: F.536, Y.544, F.595, L.598, W.599, L.602, I.819 Ligands: PC1.15, PC1.38, PC1.39, PC1.40 Ligand excluded by PLIP PC1.45: 6 residues within 4Å: Chain E: Y.570 Chain G: Y.555, F.596 Ligands: PC1.33, PC1.56, PC1.59 Ligand excluded by PLIP PC1.46: 10 residues within 4Å: Chain E: V.559, F.562, R.566, I.594 Chain H: V.69, P.70, S.73, G.76, L.77 Ligands: PC1.64 Ligand excluded by PLIP PC1.47: 6 residues within 4Å: Chain A: Y.545 Chain F: S.200, Y.201, Y.206 Ligands: PC1.10, PC1.11 Ligand excluded by PLIP PC1.48: 4 residues within 4Å: Chain F: I.213, V.220, N.224 Ligands: PC1.16 Ligand excluded by PLIP PC1.49: 3 residues within 4Å: Chain F: Y.46, Y.206, F.207 Ligand excluded by PLIP PC1.50: 5 residues within 4Å: Chain F: E.16, V.19, Q.20, I.213, L.214 Ligand excluded by PLIP PC1.51: 4 residues within 4Å: Chain F: L.137, L.140, N.156, I.157 Ligand excluded by PLIP PC1.52: 6 residues within 4Å: Chain B: F.595, E.834 Chain G: R.616 Ligands: PC1.20, PC1.23, PC1.25 Ligand excluded by PLIP PC1.56: 7 residues within 4Å: Chain G: F.537, F.596, I.820 Ligands: PC1.32, PC1.45, PC1.57, PC1.59 Ligand excluded by PLIP PC1.57: 8 residues within 4Å: Chain E: F.628 Chain G: L.540, Y.545, W.548, I.551, Y.555 Ligands: PC1.32, PC1.56 Ligand excluded by PLIP PC1.58: 4 residues within 4Å: Chain G: V.536, G.823, G.824 Ligands: PC1.59 Ligand excluded by PLIP PC1.59: 7 residues within 4Å: Chain G: L.827, I.834, E.835, Y.838 Ligands: PC1.45, PC1.56, PC1.58 Ligand excluded by PLIP PC1.60: 7 residues within 4Å: Chain E: F.567 Chain G: I.822, G.823 Chain H: V.15, A.18, M.153 Ligands: PC1.62 Ligand excluded by PLIP PC1.61: 2 residues within 4Å: Chain H: L.83, W.88 Ligand excluded by PLIP PC1.62: 7 residues within 4Å: Chain G: F.836 Chain H: A.18, I.21, F.22, I.25, W.26 Ligands: PC1.60 Ligand excluded by PLIP PC1.64: 2 residues within 4Å: Chain H: W.88 Ligands: PC1.46 Ligand excluded by PLIP

2 x CLR: CHOLESTEROL(Non-covalent)

CLR.29: 4 residues within 4Å: Chain C: Y.100, Y.130, K.133, K.138 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:Y.100, C:Y.100, C:Y.130, C:K.133, C:K.138 CLR.63: 4 residues within 4Å: Chain H: Y.100, Y.130, K.133, K.138 5 PLIP interactions: 5 interactions with chain H Hydrophobic interactions: H:Y.100, H:Y.100, H:Y.130, H:K.133, H:K.138

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

Glutamate receptor 1: AG
Glutamate receptor 2: BE
Protein cornichon homolog 2: CH
Voltage-dependent calcium channel gamma-8 subunit: DF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

G
C

B
B

E
D

C
G

H
E

D
I

F
J

Membrane

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

Glutamate receptor 2

Protein cornichon homolog 2

Voltage-dependent calcium channel gamma-8 subunit

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