SMTL ID : 6njl.1

Architecture and subunit arrangement of native AMPA receptors

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 6.70 Å

Oligo State

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

Ligands

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

NAG-NAG.1: 3 residues within 4Å: Chain A: N.63, S.65, R.92 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: R.345, N.352, Q.354, N.363 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.345 NAG-NAG.3: 4 residues within 4Å: Chain B: K.231, G.232, Y.233, N.256 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain C: N.63, S.65, D.66, R.92 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 5 residues within 4Å: Chain C: R.345, F.346, N.352, Q.354, N.363 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:R.345 NAG-NAG.6: 3 residues within 4Å: Chain D: R.206, H.234, N.256 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.206

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

ZK1.7: 9 residues within 4Å: Chain A: Y.464, P.492, L.493, T.494, R.499, G.667, S.668, T.700, Y.746 11 PLIP interactions: 11 interactions with chain A 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.700 pi-Stacking: A:Y.464, A:Y.464 Halogen bonds: A:P.492 ZK1.10: 10 residues within 4Å: Chain B: Y.471, P.499, L.500, T.501, R.506, G.674, S.675, T.707, M.729, Y.753 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:Y.471 Hydrogen bonds: B:P.499, B:T.501, B:R.506, B:R.506, B:S.675, B:S.675, B:S.675 Halogen bonds: B:P.499 ZK1.12: 9 residues within 4Å: Chain C: Y.464, P.492, L.493, T.494, R.499, G.667, S.668, T.700, Y.746 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:P.492, C:T.494, C:R.499, C:R.499, C:S.668, C:S.668, C:S.668, C:T.700 pi-Stacking: C:Y.464, C:Y.464 Halogen bonds: C:P.492 ZK1.15: 10 residues within 4Å: Chain D: Y.471, P.499, L.500, T.501, R.506, G.674, S.675, T.707, M.729, Y.753 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:Y.471 Hydrogen bonds: D:P.499, D:T.501, D:R.506, D:R.506, D:S.675, D:S.675, D:S.675 Halogen bonds: D:P.499

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

NAG.8: 3 residues within 4Å: Chain A: N.249, K.372, R.377 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.377 NAG.9: 5 residues within 4Å: Chain A: N.257, T.259, D.260, H.367, K.378 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.257, A:K.378 NAG.11: 2 residues within 4Å: Chain B: N.359, N.370 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.359 NAG.13: 3 residues within 4Å: Chain C: N.249, E.370, K.372 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:K.372 Hydrogen bonds: C:N.249, C:K.372 NAG.14: 5 residues within 4Å: Chain C: N.257, T.259, D.260, H.367, K.378 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.257, C:K.378 NAG.16: 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: AC
Glutamate receptor 2: BD
A'/C' auxiliary proteins: EG
Voltage-dependent calcium channel gamma-2 subunit: FH
11B8 scFv: IL
15F1 Fab light chain: JM
15F1 Fab heavy chain: KN

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

E
E

G
G

F
F

H
H

I
I

L
L

J
J

M
M

K
K

N
N

Membrane

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

Glutamate receptor 2

A'/C' auxiliary proteins

Voltage-dependent calcium channel gamma-2 subunit

11B8 scFv

15F1 Fab light chain

15F1 Fab heavy chain

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