SMTL ID : 6njm.1

Architecture and subunit arrangement of native AMPA receptors

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

4 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: 3 residues within 4Å: Chain A: N.57, T.59, E.60 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 4 residues within 4Å: Chain B: R.206, G.232, H.234, N.256 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.4: 3 residues within 4Å: Chain C: N.57, T.59, E.60 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.6: 6 residues within 4Å: Chain D: R.206, G.232, Y.233, H.234, A.255, N.256 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.2: 3 residues within 4Å: Chain A: N.260, K.383, A.767 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain C: N.260, K.383 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:A.767

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: 12 residues within 4Å: Chain A: E.426, Y.474, P.502, L.503, T.504, R.509, G.679, S.680, T.681, T.712, M.734, Y.758 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:P.502, A:T.504, A:R.509, A:R.509, A:S.680, A:S.680, A:T.681, A:T.681, A:T.712 Halogen bonds: A:E.426, A:P.502 ZK1.9: 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 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:E.423 ZK1.11: 12 residues within 4Å: Chain C: E.426, Y.474, P.502, L.503, T.504, R.509, G.679, S.680, T.681, T.712, M.734, Y.758 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:P.502, C:T.504, C:R.509, C:R.509, C:S.680, C:S.680, C:T.681, C:T.681, C:T.712 Halogen bonds: C:E.426, C:P.502 ZK1.13: 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 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:E.423

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

NAG.8: 5 residues within 4Å: Chain A: Q.356, N.363, Q.365, N.374, Y.396 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.396 Hydrogen bonds: A:Q.356, A:N.363, A:N.374 NAG.10: 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.12: 5 residues within 4Å: Chain C: Q.356, N.363, Q.365, N.374, Y.396 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:Y.396 Hydrogen bonds: C:Q.356, C:N.363, C:Q.365, C:N.374 NAG.14: 3 residues within 4Å: Chain D: E.354, N.359, N.370 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:E.354, 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 3: AC
Glutamate receptor 2: BD
A'-C' auxiliary proteins: EG
Voltage-dependent calcium channel gamma-2 subunit: FH
5B2 Fab Light Chain: IM
5B2 Fab Heavy Chain: JN
15F1 Fab light chain: KO
15F1 Fab heavy chain: LP

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

M
M

J
J

N
N

K
K

O
O

L
L

P
P

Membrane

We predict this structure to be a membrane protein.
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Glutamate receptor 3

Glutamate receptor 2

A'-C' auxiliary proteins

Voltage-dependent calcium channel gamma-2 subunit

5B2 Fab Light Chain

5B2 Fab Heavy Chain

15F1 Fab light chain

15F1 Fab heavy chain

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