SMTL ID : 7vtq.1

Cryo-EM structure of mouse NLRP3 (full-length) dodecamer

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-12-mer

Ligands

12 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 18 residues within 4Å: Chain A: R.187, Y.188, T.189, L.191, A.247, A.248, G.249, I.250, G.251, K.252, T.253, I.254, Y.401, P.432, L.433, W.436, H.542, M.543 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:T.189, A:T.189, A:G.249, A:I.250, A:G.251, A:K.252, A:T.253, A:T.253, A:I.254, A:Y.401 Salt bridges: A:K.252, A:H.542, A:H.542 pi-Stacking: A:F.393 ADP.3: 18 residues within 4Å: Chain B: R.187, Y.188, T.189, L.191, A.247, A.248, G.249, I.250, G.251, K.252, T.253, I.254, Y.401, P.432, L.433, W.436, H.542, M.543 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:T.189, B:T.189, B:G.249, B:I.250, B:G.251, B:K.252, B:T.253, B:T.253, B:I.254, B:Y.401 Salt bridges: B:K.252, B:H.542, B:H.542 pi-Stacking: B:F.393 ADP.5: 19 residues within 4Å: Chain C: R.187, Y.188, T.189, L.191, A.247, A.248, G.249, I.250, G.251, K.252, T.253, I.254, F.393, Y.401, P.432, L.433, W.436, H.542, M.543 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:T.189, C:T.189, C:G.249, C:I.250, C:G.251, C:K.252, C:T.253, C:T.253, C:I.254, C:Y.401 Salt bridges: C:K.252, C:H.542, C:H.542 pi-Stacking: C:F.393 ADP.7: 18 residues within 4Å: Chain D: R.187, Y.188, T.189, L.191, A.247, A.248, G.249, I.250, G.251, K.252, T.253, I.254, Y.401, P.432, L.433, W.436, H.542, M.543 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:T.189, D:T.189, D:G.249, D:I.250, D:G.251, D:K.252, D:T.253, D:T.253, D:I.254, D:Y.401 Salt bridges: D:K.252, D:H.542, D:H.542 pi-Stacking: D:F.393 ADP.9: 18 residues within 4Å: Chain E: R.187, Y.188, T.189, L.191, A.247, A.248, G.249, I.250, G.251, K.252, T.253, I.254, Y.401, P.432, L.433, W.436, H.542, M.543 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:T.189, E:T.189, E:G.249, E:I.250, E:G.251, E:K.252, E:T.253, E:T.253, E:I.254, E:Y.401 Salt bridges: E:K.252, E:H.542, E:H.542 pi-Stacking: E:F.393 ADP.11: 19 residues within 4Å: Chain F: R.187, Y.188, T.189, L.191, A.247, A.248, G.249, I.250, G.251, K.252, T.253, I.254, F.393, Y.401, P.432, L.433, W.436, H.542, M.543 14 PLIP interactions: 14 interactions with chain F Hydrogen bonds: F:T.189, F:T.189, F:G.249, F:I.250, F:G.251, F:K.252, F:T.253, F:T.253, F:I.254, F:Y.401 Salt bridges: F:K.252, F:H.542, F:H.542 pi-Stacking: F:F.393 ADP.13: 18 residues within 4Å: Chain G: R.187, Y.188, T.189, L.191, A.247, A.248, G.249, I.250, G.251, K.252, T.253, I.254, Y.401, P.432, L.433, W.436, H.542, M.543 14 PLIP interactions: 14 interactions with chain G Hydrogen bonds: G:T.189, G:T.189, G:G.249, G:I.250, G:G.251, G:K.252, G:T.253, G:T.253, G:T.253, G:I.254 Salt bridges: G:K.252, G:H.542, G:H.542 pi-Stacking: G:F.393 ADP.15: 18 residues within 4Å: Chain H: R.187, Y.188, T.189, L.191, A.247, A.248, G.249, I.250, G.251, K.252, T.253, I.254, Y.401, P.432, L.433, W.436, H.542, M.543 14 PLIP interactions: 14 interactions with chain H Hydrogen bonds: H:T.189, H:T.189, H:G.249, H:I.250, H:G.251, H:K.252, H:T.253, H:T.253, H:T.253, H:I.254 Salt bridges: H:K.252, H:H.542, H:H.542 pi-Stacking: H:F.393 ADP.17: 19 residues within 4Å: Chain I: R.187, Y.188, T.189, L.191, A.247, A.248, G.249, I.250, G.251, K.252, T.253, I.254, F.393, Y.401, P.432, L.433, W.436, H.542, M.543 14 PLIP interactions: 14 interactions with chain I Hydrogen bonds: I:T.189, I:T.189, I:G.249, I:I.250, I:G.251, I:K.252, I:T.253, I:T.253, I:T.253, I:I.254 Salt bridges: I:K.252, I:H.542, I:H.542 pi-Stacking: I:F.393 ADP.19: 18 residues within 4Å: Chain J: R.187, Y.188, T.189, L.191, A.247, A.248, G.249, I.250, G.251, K.252, T.253, I.254, Y.401, P.432, L.433, W.436, H.542, M.543 14 PLIP interactions: 14 interactions with chain J Hydrogen bonds: J:T.189, J:T.189, J:G.249, J:I.250, J:G.251, J:K.252, J:T.253, J:T.253, J:T.253, J:I.254 Salt bridges: J:K.252, J:H.542, J:H.542 pi-Stacking: J:F.393 ADP.21: 18 residues within 4Å: Chain K: R.187, Y.188, T.189, L.191, A.247, A.248, G.249, I.250, G.251, K.252, T.253, I.254, Y.401, P.432, L.433, W.436, H.542, M.543 14 PLIP interactions: 14 interactions with chain K Hydrogen bonds: K:T.189, K:T.189, K:G.249, K:I.250, K:G.251, K:K.252, K:T.253, K:T.253, K:T.253, K:I.254 Salt bridges: K:K.252, K:H.542, K:H.542 pi-Stacking: K:F.393 ADP.23: 19 residues within 4Å: Chain L: R.187, Y.188, T.189, L.191, A.247, A.248, G.249, I.250, G.251, K.252, T.253, I.254, F.393, Y.401, P.432, L.433, W.436, H.542, M.543 14 PLIP interactions: 14 interactions with chain L Hydrogen bonds: L:T.189, L:T.189, L:G.249, L:I.250, L:G.251, L:K.252, L:T.253, L:T.253, L:T.253, L:I.254 Salt bridges: L:K.252, L:H.542, L:H.542 pi-Stacking: L:F.393

12 x 7YN: 1-[4-(2-oxidanylpropan-2-yl)furan-2-yl]sulfonyl-3-(1,2,3,5-tetrahydro-s-indacen-4-yl)urea(Non-covalent)

7YN.2: 12 residues within 4Å: Chain A: G.246, A.247, A.248, R.371, V.373, I.431, F.597, R.600, L.650, E.651, Y.654, M.683 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:A.248, A:I.431, A:F.597, A:L.650, A:M.683 Hydrogen bonds: A:A.248, A:A.248, A:R.600, A:E.651 pi-Cation interactions: A:R.600 7YN.4: 12 residues within 4Å: Chain B: G.246, A.247, A.248, R.371, V.373, I.431, F.597, R.600, L.650, E.651, Y.654, M.683 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:A.248, B:I.431, B:F.597, B:L.650 Hydrogen bonds: B:A.248, B:A.248, B:R.600, B:E.651 pi-Stacking: B:Y.654 pi-Cation interactions: B:R.600 7YN.6: 11 residues within 4Å: Chain C: G.246, A.247, A.248, R.371, V.373, I.431, F.597, R.600, L.650, E.651, Y.654 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:A.248, C:I.431, C:F.597, C:L.650, C:Y.654 Hydrogen bonds: C:A.248, C:A.248, C:R.600, C:E.651, C:Y.654 pi-Cation interactions: C:R.600 7YN.8: 12 residues within 4Å: Chain D: G.246, A.247, A.248, R.371, V.373, I.431, F.597, R.600, L.650, E.651, Y.654, M.683 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:A.248, D:I.431, D:F.597, D:L.650, D:M.683 Hydrogen bonds: D:A.248, D:A.248, D:R.600, D:E.651 pi-Cation interactions: D:R.600 7YN.10: 12 residues within 4Å: Chain E: G.246, A.247, A.248, R.371, V.373, I.431, F.597, R.600, L.650, E.651, Y.654, M.683 10 PLIP interactions: 10 interactions with chain E Hydrophobic interactions: E:A.248, E:I.431, E:F.597, E:L.650 Hydrogen bonds: E:A.248, E:A.248, E:R.600, E:E.651 pi-Stacking: E:Y.654 pi-Cation interactions: E:R.600 7YN.12: 11 residues within 4Å: Chain F: G.246, A.247, A.248, R.371, V.373, I.431, F.597, R.600, L.650, E.651, Y.654 11 PLIP interactions: 11 interactions with chain F Hydrophobic interactions: F:A.248, F:I.431, F:F.597, F:L.650, F:Y.654 Hydrogen bonds: F:A.248, F:A.248, F:R.600, F:E.651, F:Y.654 pi-Cation interactions: F:R.600 7YN.14: 12 residues within 4Å: Chain G: G.246, A.247, A.248, R.371, V.373, I.431, F.597, R.600, L.650, E.651, Y.654, M.683 11 PLIP interactions: 11 interactions with chain G Hydrophobic interactions: G:A.248, G:I.431, G:F.597, G:L.650, G:M.683 Hydrogen bonds: G:A.248, G:A.248, G:R.600, G:E.651, G:Y.654 pi-Cation interactions: G:R.600 7YN.16: 12 residues within 4Å: Chain H: G.246, A.247, A.248, R.371, V.373, I.431, F.597, R.600, L.650, E.651, Y.654, M.683 11 PLIP interactions: 11 interactions with chain H Hydrophobic interactions: H:A.248, H:I.431, H:F.597, H:L.650 Hydrogen bonds: H:A.248, H:A.248, H:R.600, H:E.651, H:Y.654 pi-Stacking: H:Y.654 pi-Cation interactions: H:R.600 7YN.18: 11 residues within 4Å: Chain I: G.246, A.247, A.248, R.371, V.373, I.431, F.597, R.600, L.650, E.651, Y.654 10 PLIP interactions: 10 interactions with chain I Hydrophobic interactions: I:A.248, I:I.431, I:F.597, I:L.650, I:Y.654 Hydrogen bonds: I:A.248, I:A.248, I:R.600, I:E.651 pi-Cation interactions: I:R.600 7YN.20: 12 residues within 4Å: Chain J: G.246, A.247, A.248, R.371, V.373, I.431, F.597, R.600, L.650, E.651, Y.654, M.683 11 PLIP interactions: 11 interactions with chain J Hydrophobic interactions: J:A.248, J:I.431, J:F.597, J:L.650, J:M.683 Hydrogen bonds: J:A.248, J:A.248, J:R.600, J:E.651, J:Y.654 pi-Cation interactions: J:R.600 7YN.22: 12 residues within 4Å: Chain K: G.246, A.247, A.248, R.371, V.373, I.431, F.597, R.600, L.650, E.651, Y.654, M.683 11 PLIP interactions: 11 interactions with chain K Hydrophobic interactions: K:A.248, K:I.431, K:F.597, K:L.650 Hydrogen bonds: K:A.248, K:A.248, K:R.600, K:E.651, K:Y.654 pi-Stacking: K:Y.654 pi-Cation interactions: K:R.600 7YN.24: 11 residues within 4Å: Chain L: G.246, A.247, A.248, R.371, V.373, I.431, F.597, R.600, L.650, E.651, Y.654 10 PLIP interactions: 10 interactions with chain L Hydrophobic interactions: L:A.248, L:I.431, L:F.597, L:L.650, L:Y.654 Hydrogen bonds: L:A.248, L:A.248, L:R.600, L:E.651 pi-Cation interactions: L:R.600

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ohto, U. et al., Structural basis for the oligomerization-mediated regulation of NLRP3 inflammasome activation. Proc.Natl.Acad.Sci.USA (2022)

Release Date

2022-03-09

Peptides

NACHT, LRR and PYD domains-containing protein 3: ABCDEFGHIJKL

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

NACHT, LRR and PYD domains-containing protein 3