SMTL ID : 8ssa.1

Structure of AMPA receptor GluA2 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

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

PCW.1: 9 residues within 4Å: Chain A: V.505, F.506, G.792, G.793, L.796 Chain F: L.14, V.15, A.18, M.153 5 PLIP interactions: 3 interactions with chain F, 2 interactions with chain A Hydrophobic interactions: F:L.14, F:V.15, F:A.18, A:F.506, A:L.796 PCW.2: 10 residues within 4Å: Chain A: L.509, Y.514, M.518, V.521, F.522, L.572, F.575, N.991, Y.992, K.993 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.509, A:M.518, A:V.521, A:V.521, A:F.522, A:L.572, A:F.575 Salt bridges: A:K.993 PCW.3: 6 residues within 4Å: Chain A: I.564, F.565, Y.807, V.1013, M.1014, Y.1017 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.565, A:F.565, A:Y.1017, A:Y.1017 PCW.5: 7 residues within 4Å: Chain A: S.918, F.922, L.970 Chain B: G.792, G.793, L.796 Ligands: PCW.6 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.922, A:L.970, B:L.796 Hydrogen bonds: A:S.918 PCW.6: 19 residues within 4Å: Chain A: L.587, I.591, V.595, F.598 Chain B: F.506, L.509, Y.514, W.517, M.518, I.520, V.521, Y.524, F.565, L.568, L.572, F.575, W.596, I.789 Ligands: PCW.5 19 PLIP interactions: 15 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:W.517, B:I.520, B:V.521, B:Y.524, B:Y.524, B:Y.524, B:F.565, B:L.572, B:L.572, B:F.575, B:F.575, B:F.575, B:W.596, B:I.789, A:L.587, A:I.591, A:V.595, A:F.598 Hydrogen bonds: B:W.517 PCW.7: 11 residues within 4Å: Chain B: V.529, F.532, G.563, I.564, F.565 Chain E: V.69, P.70, S.73, I.74, L.77, L.80 10 PLIP interactions: 4 interactions with chain E, 6 interactions with chain B Hydrophobic interactions: E:I.74, E:L.77, E:L.77, E:L.80, B:V.529, B:F.532, B:I.564, B:I.564, B:I.564, B:F.565 PCW.9: 9 residues within 4Å: Chain C: V.505, F.506, G.792, G.793, L.796 Chain E: L.14, V.15, A.18, M.153 5 PLIP interactions: 3 interactions with chain E, 2 interactions with chain C Hydrophobic interactions: E:L.14, E:V.15, E:A.18, C:F.506, C:L.796 PCW.10: 10 residues within 4Å: Chain C: L.509, Y.514, M.518, V.521, F.522, L.572, F.575, N.991, Y.992, K.993 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:L.509, C:M.518, C:V.521, C:V.521, C:F.522, C:L.572, C:F.575 Salt bridges: C:K.993 PCW.11: 6 residues within 4Å: Chain C: I.564, F.565, Y.807, V.1013, M.1014, Y.1017 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:F.565, C:F.565, C:Y.1017, C:Y.1017, C:Y.1017 PCW.13: 7 residues within 4Å: Chain C: S.918, F.922, L.970 Chain D: G.792, G.793, L.796 Ligands: PCW.14 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:F.922, C:L.970, D:L.796 Hydrogen bonds: C:S.918 PCW.14: 19 residues within 4Å: Chain C: L.587, I.591, V.595, F.598 Chain D: F.506, L.509, Y.514, W.517, M.518, I.520, V.521, Y.524, F.565, L.568, L.572, F.575, W.596, I.789 Ligands: PCW.13 18 PLIP interactions: 14 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:W.517, D:I.520, D:Y.524, D:Y.524, D:Y.524, D:F.565, D:L.572, D:L.572, D:F.575, D:F.575, D:F.575, D:W.596, D:I.789, C:L.587, C:I.591, C:V.595, C:F.598 Hydrogen bonds: D:W.517 PCW.15: 10 residues within 4Å: Chain D: F.532, G.563, I.564, F.565 Chain F: V.69, P.70, S.73, I.74, L.77, L.80 10 PLIP interactions: 6 interactions with chain D, 4 interactions with chain F Hydrophobic interactions: D:F.532, D:I.564, D:I.564, D:I.564, D:F.565, F:I.74, F:L.77, F:L.77, F:L.80 Hydrogen bonds: D:I.564

4 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.4: 11 residues within 4Å: Chain A: Y.441, P.469, L.470, T.471, R.476, L.641, G.644, S.645, T.646, E.696, Y.723 12 PLIP interactions: 3 Ligand-Ligand interactions, 9 interactions with chain A Hydrogen bonds: E.4, E.4, E.4, A:P.469, A:P.469, A:T.471, A:S.645, A:T.646, A:E.696 Hydrophobic interactions: A:Y.441, A:L.641 Salt bridges: A:R.476 GLU.8: 10 residues within 4Å: Chain B: Y.441, P.469, L.470, T.471, R.476, L.641, G.644, S.645, T.646, E.696 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.8, E.8 Salt bridges: B:R.476 GLU.12: 11 residues within 4Å: Chain C: Y.441, P.469, L.470, T.471, R.476, L.641, G.644, S.645, T.646, E.696, 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:P.469, C:T.471, C:S.645, C:T.646, C:E.696, E.12, E.12, E.12 Salt bridges: C:R.476 GLU.16: 10 residues within 4Å: Chain D: Y.441, P.469, L.470, T.471, R.476, L.641, G.644, S.645, T.646, E.696 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:S.645, D:T.646, D:E.696, D:E.696, E.16, E.16 Salt bridges: D:R.476

1 x SPD: SPERMIDINE(Non-covalent)

SPD.17: 10 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, G.579 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 interactions with chain D Hydrogen bonds: C:Q.577, 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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