SMTL ID : 6njn.1

Architecture and subunit arrangement of native AMPA receptors

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-2-1-2-2-1-2-2-2-mer

Ligands

5 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: R.345, N.352, Q.354, N.363, D.385 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.352 NAG-NAG-BMA.2: 4 residues within 4Å: Chain A: N.63, S.65, R.92 Chain B: T.121 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.121 NAG-NAG-BMA.5: 3 residues within 4Å: Chain C: N.57, T.59, E.60 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:E.60 NAG-NAG-BMA.6: 6 residues within 4Å: Chain C: Q.356, N.363, Q.365, N.374, N.394, Y.396 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.7: 7 residues within 4Å: Chain C: Y.150, G.236, Y.237, H.238, G.258, N.260, K.383 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.383

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

NAG-NAG.3: 5 residues within 4Å: Chain A: N.257, T.259, D.260, H.367, K.378 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain B: G.232, Y.233, N.256 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain D: Y.143, H.234, N.256, E.377 No protein-ligand interaction detected (PLIP)

4 x ZK1: {[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2H)-yl]methyl}phosphonic acid(Non-covalent)

ZK1.9: 10 residues within 4Å: Chain A: Y.464, P.492, L.493, T.494, R.499, G.667, S.668, T.669, T.700, Y.746 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.464, A:Y.746 Hydrogen bonds: A:P.492, A:T.494, A:R.499, A:R.499, A:S.668, A:S.668, A:S.668, A:T.669, A:T.700 ZK1.11: 11 residues within 4Å: Chain B: E.423, Y.471, P.499, L.500, T.501, R.506, G.674, S.675, T.707, M.729, Y.753 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:Y.471 Hydrogen bonds: B:P.499, B:T.501, B:T.501, B:R.506, B:R.506, B:S.675, B:S.675, B:S.675, B:T.676 Halogen bonds: B:E.423 ZK1.13: 11 residues within 4Å: Chain C: Y.474, P.502, L.503, T.504, R.509, G.679, S.680, T.681, T.712, M.734, Y.758 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:Y.758 Hydrogen bonds: C:P.502, C:T.504, C:R.509, C:R.509, C:S.680, C:S.680, C:S.680, C:T.681, C:T.712 ZK1.14: 11 residues within 4Å: Chain D: E.423, Y.471, P.499, L.500, T.501, R.506, G.674, S.675, T.707, M.729, Y.753 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:Y.471, D:Y.753 Hydrogen bonds: D:P.499, D:T.501, D:T.501, D:R.506, D:R.506, D:S.675, D:S.675, D:S.675, D:T.676 Halogen bonds: D:E.423

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

NAG.10: 4 residues within 4Å: Chain A: I.224, N.249, E.370, K.372 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.249 NAG.12: 2 residues within 4Å: Chain B: N.359, N.370 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.359, B:N.370 NAG.15: 2 residues within 4Å: Chain D: N.359, N.370 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.359, D:N.370

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhao, Y. et al., Architecture and subunit arrangement of native AMPA receptors elucidated by cryo-EM. Science (2019)

Release Date

2019-04-24

Peptides

Glutamate receptor 1: A
Glutamate receptor 2: BD
Glutamate receptor 3: C
A'-C' auxiliary proteins: EG
Voltage-dependent calcium channel gamma-2 subunit: FH
11B8 scFv: I
15F1 Fab light chain: JN
15F1 Fab heavy chain: KO
5B2 Fab: LM

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D
D

C
C

E
E

G
G

F
F

H
H

I
I

J
J

N
N

K
K

O
O

L
L

M
M

Membrane

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

Glutamate receptor 2

Glutamate receptor 3

A'-C' auxiliary proteins

Voltage-dependent calcium channel gamma-2 subunit

11B8 scFv

15F1 Fab light chain

15F1 Fab heavy chain

5B2 Fab

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