SMTL ID : 8ssb.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-4-2-mer

Ligands

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

PCW.1: 14 residues within 4Å: Chain A: G.504, V.505, F.506, Y.524, F.565, L.568, I.789 Chain D: L.587, G.594, V.595 Ligands: PCW.2, PCW.3, PCW.4, PCW.7 Ligand excluded by PLIP PCW.2: 8 residues within 4Å: Chain A: V.505, F.506, L.796, L.799 Chain F: A.18, M.153 Ligands: PCW.1, PCW.32 Ligand excluded by PLIP PCW.3: 13 residues within 4Å: Chain A: L.509, Y.514, W.517, M.518, V.521, F.522, F.575, N.991, K.993, L.1006 Ligands: PCW.1, PCW.6, PCW.7 Ligand excluded by PLIP PCW.4: 8 residues within 4Å: Chain A: F.565, L.1006, V.1013, M.1014, Y.1017 Chain D: P.539, R.585 Ligands: PCW.1 Ligand excluded by PLIP PCW.5: 3 residues within 4Å: Chain A: S.918, P.921, F.922 Ligand excluded by PLIP PCW.6: 6 residues within 4Å: Chain A: F.522, Y.994, G.995, F.998, I.1003 Ligands: PCW.3 Ligand excluded by PLIP PCW.7: 2 residues within 4Å: Ligands: PCW.1, PCW.3 Ligand excluded by PLIP PCW.9: 3 residues within 4Å: Chain A: R.917, P.921, F.928 Ligand excluded by PLIP PCW.10: 9 residues within 4Å: Chain B: M.518, Y.524, I.525, L.568 Chain E: L.80, C.84 Ligands: PCW.11, PCW.12, PCW.29 Ligand excluded by PLIP PCW.11: 18 residues within 4Å: Chain A: L.587, R.590, I.591, V.595, F.598 Chain B: F.506, L.509, Y.514, W.517, M.518, V.521, Y.524, L.568, L.572, F.575, I.789 Ligands: PCW.10, PCW.12 Ligand excluded by PLIP PCW.12: 6 residues within 4Å: Chain A: V.966 Chain B: F.506, G.793, L.796 Ligands: PCW.10, PCW.11 Ligand excluded by PLIP PCW.14: 16 residues within 4Å: Chain B: R.590, G.594, V.595, F.598 Chain C: G.504, V.505, F.506, Y.524, F.565, L.568, L.572, I.789 Ligands: PCW.16, PCW.17, PCW.18, PCW.21 Ligand excluded by PLIP PCW.16: 14 residues within 4Å: Chain B: I.591, V.595 Chain C: V.505, F.506, Y.788, L.796, M.798, L.799 Chain E: L.14, A.18, M.153, L.157 Ligands: PCW.14, PCW.30 Ligand excluded by PLIP PCW.17: 14 residues within 4Å: Chain B: F.598 Chain C: L.509, Y.514, W.517, M.518, V.521, F.522, L.572, F.575, N.991, K.993 Ligands: PCW.14, PCW.20, PCW.21 Ligand excluded by PLIP PCW.18: 7 residues within 4Å: Chain B: P.539, R.585 Chain C: I.564, F.565, L.1006, Y.1017 Ligands: PCW.14 Ligand excluded by PLIP PCW.19: 2 residues within 4Å: Chain C: S.918, F.922 Ligand excluded by PLIP PCW.20: 4 residues within 4Å: Chain C: F.522, Y.994, G.995 Ligands: PCW.17 Ligand excluded by PLIP PCW.21: 2 residues within 4Å: Ligands: PCW.14, PCW.17 Ligand excluded by PLIP PCW.23: 3 residues within 4Å: Chain C: R.917, P.921, F.928 Ligand excluded by PLIP PCW.24: 10 residues within 4Å: Chain D: M.518, V.521, F.522, Y.524, I.525, L.568 Chain F: L.80, C.84 Ligands: PCW.25, PCW.26 Ligand excluded by PLIP PCW.25: 17 residues within 4Å: Chain C: R.590, G.594, F.598 Chain D: F.506, L.509, Y.514, W.517, I.520, V.521, Y.524, L.568, L.572, F.575, I.789 Ligands: PCW.24, PCW.26, PCW.27 Ligand excluded by PLIP PCW.26: 16 residues within 4Å: Chain C: L.587 Chain D: I.525, V.529, F.532, R.536, G.563, I.564, F.565 Chain F: V.69, P.70, S.73, I.74, G.76, L.77 Ligands: PCW.24, PCW.25 Ligand excluded by PLIP PCW.27: 6 residues within 4Å: Chain C: V.595 Chain D: V.505, F.506, G.793, L.796 Ligands: PCW.25 Ligand excluded by PLIP PCW.29: 14 residues within 4Å: Chain A: L.587 Chain B: I.525, V.529, F.532, G.563, I.564, F.565 Chain E: V.69, P.70, S.73, I.74, G.76, L.77 Ligands: PCW.10 Ligand excluded by PLIP PCW.30: 3 residues within 4Å: Chain E: L.157, V.158 Ligands: PCW.16 Ligand excluded by PLIP PCW.31: 3 residues within 4Å: Chain E: F.147, L.150, Y.151 Ligand excluded by PLIP PCW.32: 3 residues within 4Å: Chain F: L.157, V.158 Ligands: PCW.2 Ligand excluded by PLIP PCW.33: 2 residues within 4Å: Chain F: F.147, Y.151 Ligand excluded by PLIP

4 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.8: 11 residues within 4Å: Chain A: Y.441, P.469, L.470, T.471, L.641, G.644, S.645, T.646, E.696, M.699, Y.723 12 PLIP interactions: 9 interactions with chain A, 3 Ligand-Ligand interactions Hydrophobic interactions: A:Y.441, A:L.641 Hydrogen bonds: A:P.469, A:P.469, A:T.471, A:S.645, A:T.646, A:E.696, E.8, E.8, E.8 Salt bridges: A:R.476 GLU.13: 10 residues within 4Å: Chain B: Y.441, T.471, R.476, L.641, D.642, G.644, S.645, T.646, E.696, Y.723 10 PLIP interactions: 8 interactions with chain B, 2 Ligand-Ligand interactions Hydrophobic interactions: B:Y.441, B:Y.441 Hydrogen bonds: B:T.471, B:S.645, B:T.646, B:E.696, B:E.696, E.13, E.13 Salt bridges: B:R.476 GLU.22: 11 residues within 4Å: Chain C: Y.441, P.469, L.470, T.471, L.641, G.644, S.645, T.646, E.696, M.699, Y.723 12 PLIP interactions: 9 interactions with chain C, 3 Ligand-Ligand interactions Hydrophobic interactions: C:Y.441, C:L.641 Hydrogen bonds: C:P.469, C:T.471, C:S.645, C:S.645, C:T.646, C:E.696, E.22, E.22, E.22 Salt bridges: C:R.476 GLU.28: 10 residues within 4Å: Chain D: Y.441, T.471, R.476, L.641, D.642, G.644, S.645, T.646, E.696, Y.723 10 PLIP interactions: 8 interactions with chain D, 2 Ligand-Ligand interactions Hydrophobic interactions: D:Y.441, D:Y.441 Hydrogen bonds: D:T.471, D:G.644, D:S.645, D:T.646, D:E.696, E.28, E.28 Salt bridges: D:R.476

1 x SPD: SPERMIDINE(Non-covalent)

SPD.15: 9 residues within 4Å: Chain A: Q.577, G.579 Chain B: Q.577, Q.578, G.579 Chain C: Q.577, G.579 Chain D: Q.577, Q.578 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:Q.577 Hydrogen bonds: A:Q.577, A:G.579, D: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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