SMTL ID : 8ss2.1

Structure of AMPA receptor GluA2 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: 12 residues within 4Å: Chain A: E.393, Y.396, Y.441, P.469, T.471, R.476, L.641, G.644, S.645, E.696, M.699, Y.723 7 PLIP interactions: 7 interactions with chain A 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 ZK1.12: 12 residues within 4Å: Chain B: E.393, Y.396, Y.441, P.469, L.470, T.471, R.476, G.644, S.645, T.677, M.699, Y.723 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:Y.723 Hydrogen bonds: B:P.469, B:T.471, B:R.476, B:R.476, B:S.645, B:S.645, B:S.645, B:T.677 pi-Stacking: B:Y.441, B:Y.441 ZK1.17: 12 residues within 4Å: Chain C: E.393, Y.396, Y.441, P.469, T.471, R.476, L.641, G.644, S.645, E.696, M.699, Y.723 7 PLIP interactions: 7 interactions with chain C 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 ZK1.27: 12 residues within 4Å: Chain D: E.393, Y.396, Y.441, P.469, L.470, T.471, R.476, G.644, S.645, T.677, M.699, Y.723 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:Y.723 Hydrogen bonds: D:P.469, D:T.471, D:R.476, D:R.476, D:S.645, D:S.645, D:S.645, D:T.677 pi-Stacking: D:Y.441, D:Y.441

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

PCW.2: 5 residues within 4Å: Chain A: F.506, G.793 Chain D: V.595 Chain F: M.11 Ligands: PCW.7 Ligand excluded by PLIP PCW.3: 11 residues within 4Å: Chain A: Y.854, E.856, K.993, Y.994, G.995, W.996, A.999, F.1000, A.1002, I.1003 Ligands: AJP.6 Ligand excluded by PLIP PCW.4: 4 residues within 4Å: Chain A: S.918, F.922 Ligands: CLR.5, PCW.15 Ligand excluded by PLIP PCW.7: 12 residues within 4Å: Chain A: G.504, F.506, L.509, W.517, V.521, Y.524, L.572, F.575, I.789 Chain D: G.594 Ligands: PCW.2, AJP.6 Ligand excluded by PLIP PCW.8: 4 residues within 4Å: Chain A: E.895, R.917, T.920, P.921 Ligand excluded by PLIP PCW.9: 7 residues within 4Å: Chain A: P.539, R.585, L.587 Chain B: F.565, E.804, Y.807 Ligands: PCW.14 Ligand excluded by PLIP PCW.10: 2 residues within 4Å: Chain A: I.942, R.943 Ligand excluded by PLIP PCW.13: 15 residues within 4Å: Chain A: V.595, F.598 Chain B: F.506, L.509, Y.514, W.517, V.521, Y.524, F.565, L.568, L.572, F.575, M.576, I.789 Ligands: PCW.15 Ligand excluded by PLIP PCW.14: 9 residues within 4Å: Chain B: F.532, R.536, I.564 Chain E: V.69, S.73, I.74, L.77, L.80 Ligands: PCW.9 Ligand excluded by PLIP PCW.15: 6 residues within 4Å: Chain A: V.595 Chain B: F.506 Ligands: PCW.4, CLR.5, PCW.13, PCW.16 Ligand excluded by PLIP PCW.16: 2 residues within 4Å: Ligands: CLR.5, PCW.15 Ligand excluded by PLIP PCW.18: 5 residues within 4Å: Chain B: V.595 Chain C: F.506, Y.788 Chain E: M.11 Ligands: PCW.23 Ligand excluded by PLIP PCW.19: 10 residues within 4Å: Chain C: Y.854, E.856, K.993, Y.994, G.995, W.996, F.1000, A.1002, I.1003 Ligands: AJP.22 Ligand excluded by PLIP PCW.20: 4 residues within 4Å: Chain C: S.918, F.922 Ligands: CLR.21, PCW.30 Ligand excluded by PLIP PCW.23: 13 residues within 4Å: Chain B: G.594, F.598 Chain C: G.504, F.506, L.509, W.517, V.521, Y.524, L.572, F.575, I.789 Ligands: PCW.18, AJP.22 Ligand excluded by PLIP PCW.24: 3 residues within 4Å: Chain C: E.895, R.917, P.921 Ligand excluded by PLIP PCW.25: 9 residues within 4Å: Chain C: P.539, R.585, S.586, L.587 Chain D: F.565, L.568, E.804, Y.807 Ligands: PCW.29 Ligand excluded by PLIP PCW.26: 1 residues within 4Å: Chain C: R.943 Ligand excluded by PLIP PCW.28: 15 residues within 4Å: Chain C: V.595, F.598 Chain D: F.506, L.509, Y.514, W.517, V.521, Y.524, F.565, L.568, W.569, L.572, F.575, I.789 Ligands: PCW.30 Ligand excluded by PLIP PCW.29: 10 residues within 4Å: Chain D: F.532, R.536, I.564 Chain F: V.69, P.70, S.73, I.74, L.77, L.80 Ligands: PCW.25 Ligand excluded by PLIP PCW.30: 5 residues within 4Å: Chain D: F.506 Ligands: PCW.20, CLR.21, PCW.28, PCW.31 Ligand excluded by PLIP PCW.31: 2 residues within 4Å: Ligands: CLR.21, PCW.30 Ligand excluded by PLIP PCW.32: 1 residues within 4Å: Chain E: L.150 Ligand excluded by PLIP PCW.33: 3 residues within 4Å: Chain E: Y.151, V.154, V.158 Ligand excluded by PLIP PCW.34: 1 residues within 4Å: Chain F: L.150 Ligand excluded by PLIP PCW.35: 3 residues within 4Å: Chain F: Y.151, V.154, V.158 Ligand excluded by PLIP

2 x CLR: CHOLESTEROL(Non-covalent)

CLR.5: 11 residues within 4Å: Chain A: L.959, L.962, S.963, V.966, L.970 Chain B: Y.788, V.791, G.792 Ligands: PCW.4, PCW.15, PCW.16 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.959, A:L.962, A:V.966, A:L.970, B:Y.788 CLR.21: 11 residues within 4Å: Chain C: L.959, L.962, S.963, V.966, L.970 Chain D: Y.788, V.791, G.792 Ligands: PCW.20, PCW.30, PCW.31 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:L.959, C:L.962, C:V.966, C:L.970, D:Y.788

2 x AJP: Digitonin(Non-covalent)

AJP.6: 7 residues within 4Å: Chain A: Y.514, M.518, V.521, F.522, L.1006 Ligands: PCW.3, PCW.7 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.514, A:M.518, A:L.1006 Hydrogen bonds: A:Y.514, A:Y.514 AJP.22: 8 residues within 4Å: Chain C: Y.514, W.517, M.518, V.521, F.522, L.1006 Ligands: PCW.19, PCW.23 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:Y.514, C:Y.514, C:M.518, C:V.521, C:L.1006 Hydrogen bonds: C:Y.514

1 x SPD: SPERMIDINE(Non-covalent)

SPD.11: 9 residues within 4Å: Chain A: Q.577, Q.578, G.579 Chain B: Q.577, G.579 Chain C: Q.577, G.579 Chain D: Q.577, G.579 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:G.579, A:Q.577, A: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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