SMTL ID : 8ss3.1

Structure of LBD-TMD of AMPA receptor GluA2 in complex with auxiliary subunits TARP gamma-5 and cornichon-2 bound to competitive antagonist ZK and channel blocker spermidine (closed state)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-2-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)

ZK1.1: 13 residues within 4Å: Chain A: E.393, Y.396, Y.441, P.469, T.471, R.476, L.641, G.644, S.645, T.677, E.696, M.699, Y.723 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.441, A:Y.441 Hydrogen bonds: A:P.469, A:T.471, A:T.471, A:R.476, A:R.476, A:S.645 pi-Stacking: A:Y.441 ZK1.21: 13 residues within 4Å: Chain B: E.393, Y.441, P.469, L.470, T.471, R.476, G.644, S.645, T.677, E.696, T.698, M.699, Y.723 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:P.469, B:T.471, B:T.471, B:R.476, B:R.476, B:S.645, B:S.645, B:T.677 pi-Stacking: B:Y.441, B:Y.441 ZK1.31: 13 residues within 4Å: Chain C: E.393, Y.396, Y.441, P.469, T.471, R.476, L.641, G.644, S.645, T.677, E.696, M.699, Y.723 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:Y.441, C:Y.441 Hydrogen bonds: C:P.469, C:T.471, C:T.471, C:R.476, C:R.476, C:S.645 pi-Stacking: C:Y.441 ZK1.47: 12 residues within 4Å: Chain D: E.393, Y.441, P.469, T.471, R.476, G.644, S.645, T.677, E.696, T.698, M.699, Y.723 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:P.469, D:T.471, D:T.471, D:R.476, D:R.476, D:S.645, D:S.645, D:T.677 pi-Stacking: D:Y.441, D:Y.441

50 x PCW: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)(Non-functional Binders)

PCW.2: 16 residues within 4Å: Chain A: G.504, V.505, F.506, I.789, G.792, G.793, L.796, M.798 Chain D: V.595 Chain F: L.14, A.18, S.19, F.22, L.157 Ligands: CLR.12, PCW.14 Ligand excluded by PLIP PCW.3: 11 residues within 4Å: Chain A: Y.854, Y.994, G.995, W.996, F.998, A.999, F.1000, A.1002, I.1003, L.1006 Ligands: AJP.10 Ligand excluded by PLIP PCW.4: 12 residues within 4Å: Chain A: I.525, V.529, L.828, L.831, L.1006, E.1009, S.1010, V.1013, M.1014, Y.1017, K.1021 Ligands: PCW.5 Ligand excluded by PLIP PCW.5: 14 residues within 4Å: Chain A: V.521, Y.524, I.525, R.536, N.560, I.564, F.565, L.568, Y.1017 Chain D: Y.540, L.587 Ligands: PCW.4, CLR.12, PCW.14 Ligand excluded by PLIP PCW.6: 1 residues within 4Å: Ligands: AJP.16 Ligand excluded by PLIP PCW.8: 4 residues within 4Å: Chain A: F.931, N.938, I.942 Ligands: PCW.17 Ligand excluded by PLIP PCW.9: 1 residues within 4Å: Ligands: CLR.7 Ligand excluded by PLIP PCW.13: 4 residues within 4Å: Chain A: L.802, C.806, Y.807, R.810 Ligand excluded by PLIP PCW.14: 13 residues within 4Å: Chain A: F.506, L.509, W.517, I.520, Y.524, L.572, F.575, M.576 Chain D: G.594, F.598 Ligands: PCW.2, PCW.5, AJP.10 Ligand excluded by PLIP PCW.15: 2 residues within 4Å: Chain A: R.917 Ligands: CLR.7 Ligand excluded by PLIP PCW.17: 1 residues within 4Å: Ligands: PCW.8 Ligand excluded by PLIP PCW.18: 11 residues within 4Å: Chain A: I.948, V.952, F.956 Chain B: L.799, L.802, F.805, C.806 Ligands: CLR.7, AJP.16, PCW.20, PCW.28 Ligand excluded by PLIP PCW.20: 11 residues within 4Å: Chain A: F.537, S.538, F.951, I.955, L.959 Chain B: G.795, M.798, L.799, A.801, L.802 Ligands: PCW.18 Ligand excluded by PLIP PCW.22: 11 residues within 4Å: Chain B: M.518, F.522, I.525, I.564, L.568 Chain E: L.80 Ligands: PCW.23, PCW.24, PCW.25, PCW.26, PCW.56 Ligand excluded by PLIP PCW.23: 19 residues within 4Å: Chain A: R.590, G.594, V.595, F.598 Chain B: F.506, L.509, Y.514, W.517, I.520, V.521, Y.524, F.565, L.572, F.575, M.576, I.789 Ligands: PCW.22, PCW.25, PCW.26 Ligand excluded by PLIP PCW.24: 13 residues within 4Å: Chain B: I.525, V.529, F.532, G.563, I.564 Chain E: V.69, P.70, S.73, I.74, L.77, L.80 Ligands: PCW.22, PCW.26 Ligand excluded by PLIP PCW.25: 10 residues within 4Å: Chain A: V.595 Chain B: V.505, F.506, I.789, G.792 Ligands: AJP.16, PCW.22, PCW.23, PCW.26, PCW.28 Ligand excluded by PLIP PCW.26: 12 residues within 4Å: Chain A: P.539, R.585, S.586, L.587 Chain B: F.565, L.568, I.803, Y.807 Ligands: PCW.22, PCW.23, PCW.24, PCW.25 Ligand excluded by PLIP PCW.27: 3 residues within 4Å: Chain B: C.806, Y.807, R.810 Ligand excluded by PLIP PCW.28: 3 residues within 4Å: Ligands: AJP.16, PCW.18, PCW.25 Ligand excluded by PLIP PCW.29: 14 residues within 4Å: Chain B: Y.540, L.587 Chain C: V.521, Y.524, I.525, R.536, N.560, I.564, F.565, L.568, Y.1017 Ligands: PCW.30, PCW.34, CLR.41 Ligand excluded by PLIP PCW.30: 14 residues within 4Å: Chain B: G.594, F.598 Chain C: F.506, L.509, W.517, I.520, V.521, Y.524, L.572, F.575, M.576 Ligands: PCW.29, PCW.32, AJP.39 Ligand excluded by PLIP PCW.32: 17 residues within 4Å: Chain B: I.591, V.595 Chain C: G.504, V.505, F.506, I.789, G.792, G.793, L.796, M.798 Chain E: L.14, A.18, S.19, F.22, L.157 Ligands: PCW.30, CLR.41 Ligand excluded by PLIP PCW.33: 11 residues within 4Å: Chain C: Y.854, Y.994, G.995, W.996, F.998, A.999, F.1000, A.1002, I.1003, L.1006 Ligands: AJP.39 Ligand excluded by PLIP PCW.34: 11 residues within 4Å: Chain C: I.525, V.529, L.828, L.1006, E.1009, S.1010, V.1013, M.1014, Y.1017, K.1021 Ligands: PCW.29 Ligand excluded by PLIP PCW.35: 1 residues within 4Å: Ligands: AJP.44 Ligand excluded by PLIP PCW.37: 4 residues within 4Å: Chain C: F.931, N.938, I.942 Ligands: PCW.45 Ligand excluded by PLIP PCW.38: 1 residues within 4Å: Ligands: CLR.36 Ligand excluded by PLIP PCW.42: 4 residues within 4Å: Chain C: L.802, C.806, Y.807, R.810 Ligand excluded by PLIP PCW.43: 2 residues within 4Å: Chain C: R.917 Ligands: CLR.36 Ligand excluded by PLIP PCW.45: 1 residues within 4Å: Ligands: PCW.37 Ligand excluded by PLIP PCW.46: 11 residues within 4Å: Chain C: F.537, S.538, F.951, I.955, L.959 Chain D: G.795, M.798, L.799, A.801, L.802 Ligands: PCW.54 Ligand excluded by PLIP PCW.48: 12 residues within 4Å: Chain D: M.518, F.522, Y.524, I.525, I.564, L.568 Chain F: L.80 Ligands: PCW.49, PCW.50, PCW.51, PCW.52, PCW.65 Ligand excluded by PLIP PCW.49: 20 residues within 4Å: Chain C: R.590, G.594, V.595, F.598 Chain D: F.506, L.509, Y.514, W.517, I.520, V.521, Y.524, F.565, W.569, L.572, F.575, M.576, I.789 Ligands: PCW.48, PCW.51, PCW.52 Ligand excluded by PLIP PCW.50: 13 residues within 4Å: Chain D: I.525, V.529, F.532, G.563, I.564 Chain F: V.69, P.70, S.73, I.74, L.77, L.80 Ligands: PCW.48, PCW.52 Ligand excluded by PLIP PCW.51: 10 residues within 4Å: Chain C: V.595 Chain D: V.505, F.506, I.789, G.792 Ligands: AJP.44, PCW.48, PCW.49, PCW.52, PCW.55 Ligand excluded by PLIP PCW.52: 10 residues within 4Å: Chain C: P.539, R.585, S.586, L.587 Chain D: F.565, L.568 Ligands: PCW.48, PCW.49, PCW.50, PCW.51 Ligand excluded by PLIP PCW.53: 3 residues within 4Å: Chain D: C.806, Y.807, R.810 Ligand excluded by PLIP PCW.54: 15 residues within 4Å: Chain C: I.948, V.952, F.956, L.959 Chain D: G.792, G.795, L.796, L.799, L.802, F.805, C.806 Ligands: CLR.36, AJP.44, PCW.46, PCW.55 Ligand excluded by PLIP PCW.55: 3 residues within 4Å: Ligands: AJP.44, PCW.51, PCW.54 Ligand excluded by PLIP PCW.56: 2 residues within 4Å: Chain E: L.83 Ligands: PCW.22 Ligand excluded by PLIP PCW.57: 2 residues within 4Å: Chain E: L.150, V.158 Ligand excluded by PLIP PCW.58: 5 residues within 4Å: Chain E: F.147, L.150, Y.151, V.158, S.159 Ligand excluded by PLIP PCW.59: 1 residues within 4Å: Ligands: PCW.60 Ligand excluded by PLIP PCW.60: 5 residues within 4Å: Chain E: I.21, F.22, I.25, W.26 Ligands: PCW.59 Ligand excluded by PLIP PCW.61: 2 residues within 4Å: Chain F: L.150, V.158 Ligand excluded by PLIP PCW.62: 5 residues within 4Å: Chain F: F.147, L.150, Y.151, V.158, S.159 Ligand excluded by PLIP PCW.63: 1 residues within 4Å: Ligands: PCW.64 Ligand excluded by PLIP PCW.64: 5 residues within 4Å: Chain F: I.21, F.22, I.25, W.26 Ligands: PCW.63 Ligand excluded by PLIP PCW.65: 2 residues within 4Å: Chain F: L.83 Ligands: PCW.48 Ligand excluded by PLIP

4 x CLR: CHOLESTEROL(Non-covalent)

CLR.7: 9 residues within 4Å: Chain A: F.928, I.932, L.936, R.946, L.949, F.956 Ligands: PCW.9, PCW.15, PCW.18 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.932, A:I.932, A:L.936, A:L.949 CLR.12: 7 residues within 4Å: Chain A: L.796, V.800, I.803, E.804 Chain D: I.591 Ligands: PCW.2, PCW.5 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:L.796, A:V.800, A:V.800, A:I.803, A:I.803, A:E.804, D:I.591 CLR.36: 9 residues within 4Å: Chain C: F.928, I.932, L.936, R.946, L.949, F.956 Ligands: PCW.38, PCW.43, PCW.54 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:F.928, C:I.932, C:I.932, C:L.936, C:L.949 Hydrogen bonds: C:R.946 CLR.41: 7 residues within 4Å: Chain B: I.591 Chain C: L.796, V.800, I.803, E.804 Ligands: PCW.29, PCW.32 8 PLIP interactions: 2 interactions with chain B, 6 interactions with chain C Hydrophobic interactions: B:I.591, B:I.591, C:L.796, C:V.800, C:V.800, C:I.803, C:I.803, C:E.804

6 x AJP: Digitonin(Non-covalent)

AJP.10: 8 residues within 4Å: Chain A: Y.514, M.518, V.521, F.522, Y.992, K.993 Ligands: PCW.3, PCW.14 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.514, A:M.518, A:V.521 Hydrogen bonds: A:Y.992 AJP.11: 3 residues within 4Å: Chain A: L.840, G.844, S.848 No protein-ligand interaction detected (PLIP) AJP.16: 14 residues within 4Å: Chain A: S.918, F.922, L.959, L.962, V.966, L.970 Chain B: V.505, Y.788, V.791, G.792 Ligands: PCW.6, PCW.18, PCW.25, PCW.28 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:F.922, A:L.959, A:V.966, A:L.970, B:Y.788, B:Y.788, B:V.791 Hydrogen bonds: A:S.918, B:Y.788 AJP.39: 8 residues within 4Å: Chain C: Y.514, W.517, M.518, V.521, Y.992, K.993 Ligands: PCW.30, PCW.33 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:Y.514, C:M.518, C:V.521 Hydrogen bonds: C:Y.514 AJP.40: 4 residues within 4Å: Chain C: L.840, G.844, I.845, S.848 No protein-ligand interaction detected (PLIP) AJP.44: 15 residues within 4Å: Chain C: S.918, F.922, L.959, L.962, V.966, L.970 Chain D: V.505, Y.788, V.791, G.792, G.795 Ligands: PCW.35, PCW.51, PCW.54, PCW.55 9 PLIP interactions: 4 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:Y.788, D:Y.788, D:V.791, C:F.922, C:L.959, C:V.966, C:L.970 Hydrogen bonds: D:Y.788, C:S.918

1 x SPD: SPERMIDINE(Non-covalent)

SPD.19: 7 residues within 4Å: Chain A: Q.577, G.579 Chain B: Q.577, G.579 Chain C: Q.577, G.579 Chain D: Q.577 4 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A, 1 interactions with chain D Hydrogen bonds: C:Q.577, C:G.579, D:Q.577 Hydrophobic interactions: A:Q.577

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gangwar, S.P. et al., Modulation of GluA2-gamma 5 synaptic complex desensitization, polyamine block and antiepileptic perampanel inhibition by auxiliary subunit cornichon-2. Nat.Struct.Mol.Biol. (2023)

Release Date

2023-09-06

Peptides

Glutamate receptor 2, Voltage-dependent calcium channel gamma-5 subunit chimera: ABCD
Protein cornichon homolog 2: EF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Membrane

We predict this structure to be a membrane protein.
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Glutamate receptor 2, Voltage-dependent calcium channel gamma-5 subunit chimera

Protein cornichon homolog 2

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