SMTL ID : 8ej4.1

Cryo-EM structure of the active NLRP3 inflammasome disk

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-10-10-mer

Ligands

10 x AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER(Non-covalent)

AGS.1: 20 residues within 4Å: Chain A: I.19, R.22, R.35, Y.36, T.37, L.39, A.96, G.97, I.98, G.99, K.100, T.101, I.102, R.219, F.241, Y.249, P.280, L.281, W.284 Ligands: MG.2 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:R.22, A:R.35, A:T.37, A:T.37, A:T.37, A:G.97, A:I.98, A:G.99, A:K.100, A:K.100, A:T.101, A:I.102, A:R.219, A:Y.249 Salt bridges: A:K.100 AGS.3: 20 residues within 4Å: Chain B: I.19, R.22, R.35, Y.36, T.37, L.39, A.96, G.97, I.98, G.99, K.100, T.101, I.102, R.219, F.241, Y.249, P.280, L.281, W.284 Ligands: MG.4 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:R.22, B:R.35, B:T.37, B:T.37, B:T.37, B:G.97, B:I.98, B:G.99, B:K.100, B:K.100, B:T.101, B:I.102, B:R.219, B:Y.249 Salt bridges: B:K.100 AGS.5: 20 residues within 4Å: Chain C: I.19, R.22, R.35, Y.36, T.37, L.39, A.96, G.97, I.98, G.99, K.100, T.101, I.102, R.219, F.241, Y.249, P.280, L.281, W.284 Ligands: MG.6 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:R.22, C:R.35, C:T.37, C:T.37, C:T.37, C:G.97, C:I.98, C:G.99, C:K.100, C:K.100, C:T.101, C:I.102, C:R.219, C:Y.249 Salt bridges: C:K.100 AGS.7: 20 residues within 4Å: Chain D: I.19, R.22, R.35, Y.36, T.37, L.39, A.96, G.97, I.98, G.99, K.100, T.101, I.102, R.219, F.241, Y.249, P.280, L.281, W.284 Ligands: MG.8 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:R.22, D:R.35, D:T.37, D:T.37, D:T.37, D:G.97, D:I.98, D:G.99, D:K.100, D:K.100, D:T.101, D:I.102, D:R.219, D:Y.249 Salt bridges: D:K.100 AGS.9: 20 residues within 4Å: Chain E: I.19, R.22, R.35, Y.36, T.37, L.39, A.96, G.97, I.98, G.99, K.100, T.101, I.102, R.219, F.241, Y.249, P.280, L.281, W.284 Ligands: MG.10 15 PLIP interactions: 15 interactions with chain E Hydrogen bonds: E:R.22, E:R.35, E:T.37, E:T.37, E:T.37, E:G.97, E:I.98, E:G.99, E:K.100, E:K.100, E:T.101, E:I.102, E:R.219, E:Y.249 Salt bridges: E:K.100 AGS.11: 20 residues within 4Å: Chain F: I.19, R.22, R.35, Y.36, T.37, L.39, A.96, G.97, I.98, G.99, K.100, T.101, I.102, R.219, F.241, Y.249, P.280, L.281, W.284 Ligands: MG.12 15 PLIP interactions: 15 interactions with chain F Hydrogen bonds: F:R.22, F:R.35, F:T.37, F:T.37, F:T.37, F:G.97, F:I.98, F:G.99, F:K.100, F:K.100, F:T.101, F:I.102, F:R.219, F:Y.249 Salt bridges: F:K.100 AGS.13: 20 residues within 4Å: Chain G: I.19, R.22, R.35, Y.36, T.37, L.39, A.96, G.97, I.98, G.99, K.100, T.101, I.102, R.219, F.241, Y.249, P.280, L.281, W.284 Ligands: MG.14 15 PLIP interactions: 15 interactions with chain G Hydrogen bonds: G:R.22, G:R.35, G:T.37, G:T.37, G:T.37, G:G.97, G:I.98, G:G.99, G:K.100, G:K.100, G:T.101, G:I.102, G:R.219, G:Y.249 Salt bridges: G:K.100 AGS.15: 20 residues within 4Å: Chain H: I.19, R.22, R.35, Y.36, T.37, L.39, A.96, G.97, I.98, G.99, K.100, T.101, I.102, R.219, F.241, Y.249, P.280, L.281, W.284 Ligands: MG.16 16 PLIP interactions: 16 interactions with chain H Hydrogen bonds: H:R.22, H:R.35, H:T.37, H:T.37, H:T.37, H:G.97, H:I.98, H:G.99, H:K.100, H:K.100, H:T.101, H:T.101, H:I.102, H:R.219, H:Y.249 Salt bridges: H:K.100 AGS.17: 20 residues within 4Å: Chain I: I.19, R.22, R.35, Y.36, T.37, L.39, A.96, G.97, I.98, G.99, K.100, T.101, I.102, R.219, F.241, Y.249, P.280, L.281, W.284 Ligands: MG.18 15 PLIP interactions: 15 interactions with chain I Hydrogen bonds: I:R.22, I:R.35, I:T.37, I:T.37, I:T.37, I:G.97, I:I.98, I:G.99, I:K.100, I:K.100, I:T.101, I:I.102, I:R.219, I:Y.249 Salt bridges: I:K.100 AGS.19: 20 residues within 4Å: Chain J: I.19, R.22, R.35, Y.36, T.37, L.39, A.96, G.97, I.98, G.99, K.100, T.101, I.102, R.219, F.241, Y.249, P.280, L.281, W.284 Ligands: MG.20 15 PLIP interactions: 15 interactions with chain J Hydrogen bonds: J:R.22, J:R.35, J:T.37, J:T.37, J:T.37, J:G.97, J:I.98, J:G.99, J:K.100, J:K.100, J:T.101, J:I.102, J:R.219, J:Y.249 Salt bridges: J:K.100

10 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: K.100, T.101, D.170 Ligands: AGS.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:T.101, A:D.170 MG.4: 4 residues within 4Å: Chain B: K.100, T.101, D.170 Ligands: AGS.3 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:T.101, B:D.170 MG.6: 4 residues within 4Å: Chain C: K.100, T.101, D.170 Ligands: AGS.5 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:T.101, C:D.170 MG.8: 4 residues within 4Å: Chain D: K.100, T.101, D.170 Ligands: AGS.7 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:T.101, D:D.170 MG.10: 4 residues within 4Å: Chain E: K.100, T.101, D.170 Ligands: AGS.9 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:T.101, E:D.170 MG.12: 4 residues within 4Å: Chain F: K.100, T.101, D.170 Ligands: AGS.11 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:T.101, F:D.170 MG.14: 4 residues within 4Å: Chain G: K.100, T.101, D.170 Ligands: AGS.13 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:T.101, G:D.170 MG.16: 4 residues within 4Å: Chain H: K.100, T.101, D.170 Ligands: AGS.15 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:T.101, H:D.170 MG.18: 4 residues within 4Å: Chain I: K.100, T.101, D.170 Ligands: AGS.17 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:T.101, I:D.170 MG.20: 4 residues within 4Å: Chain J: K.100, T.101, D.170 Ligands: AGS.19 2 PLIP interactions: 2 interactions with chain J Metal complexes: J:T.101, J:D.170

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xiao, L. et al., Cryo-EM structures of the active NLRP3 inflammasome disc. Nature (2023)

Release Date

2022-12-14

Peptides

NACHT, LRR and PYD domains-containing protein 3: ABCDEFGHIJ
Serine/threonine-protein kinase Nek7: KLMNOPQRST

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

N
N

O
O

P
P

Q
Q

R
R

S
S

T
T

NACHT, LRR and PYD domains-containing protein 3

Serine/threonine-protein kinase Nek7