SMTL ID : 8swk.1

Cryo-EM structure of NLRP3 closed hexamer

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

6 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.1: 13 residues within 4Å: Chain A: A.101, A.102, I.285, L.287, V.288, T.313, Y.317, I.448, F.449, R.452, L.502, Y.506, M.535 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:I.285, A:L.287, A:V.288, A:T.313, A:F.449, A:F.449, A:Y.506 Hydrogen bonds: A:A.102, A:R.452 7YN.3: 13 residues within 4Å: Chain B: A.101, A.102, I.285, L.287, V.288, T.313, Y.317, I.448, F.449, R.452, L.502, Y.506, M.535 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:I.285, B:L.287, B:V.288, B:T.313, B:F.449, B:F.449, B:L.502, B:Y.506 Hydrogen bonds: B:A.102, B:A.102, B:R.452, B:R.452 7YN.5: 13 residues within 4Å: Chain C: A.101, A.102, I.285, L.287, V.288, T.313, Y.317, I.448, F.449, R.452, L.502, Y.506, M.535 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:I.285, C:L.287, C:V.288, C:T.313, C:Y.317, C:F.449, C:F.449, C:Y.506 Hydrogen bonds: C:A.102, C:A.102, C:R.452, C:R.452 7YN.7: 12 residues within 4Å: Chain D: A.101, A.102, I.285, V.288, T.313, Y.317, I.448, F.449, R.452, L.502, Y.506, M.535 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:A.102, D:I.285, D:V.288, D:T.313, D:Y.317, D:F.449, D:F.449, D:Y.506 Hydrogen bonds: D:A.102, D:A.102, D:R.452, D:R.452 7YN.9: 13 residues within 4Å: Chain E: A.101, A.102, I.285, L.287, V.288, T.313, Y.317, I.448, F.449, R.452, L.502, Y.506, M.535 13 PLIP interactions: 13 interactions with chain E Hydrophobic interactions: E:I.285, E:L.287, E:V.288, E:T.313, E:Y.317, E:F.449, E:F.449, E:L.502, E:Y.506 Hydrogen bonds: E:A.102, E:A.102, E:R.452, E:R.452 7YN.11: 14 residues within 4Å: Chain F: A.101, A.102, R.225, P.226, I.285, V.288, T.313, Y.317, I.448, F.449, R.452, L.502, Y.506, M.535 12 PLIP interactions: 12 interactions with chain F Hydrophobic interactions: F:A.102, F:I.285, F:V.288, F:T.313, F:Y.317, F:F.449, F:F.449, F:Y.506 Hydrogen bonds: F:A.102, F:A.102, F:R.452, F:R.452

6 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.2: 16 residues within 4Å: Chain A: I.25, Y.42, T.43, L.45, G.103, G.105, T.107, I.108, H.134, R.136, D.176, E.180, F.247, P.286, W.290, H.396 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:T.43, A:T.43, A:G.103, A:T.107, A:T.107, A:T.107, A:R.136, A:D.176, A:D.176, A:W.290 Salt bridges: A:H.396 pi-Stacking: A:F.247 ATP.4: 16 residues within 4Å: Chain B: I.25, Y.42, T.43, L.45, G.103, G.105, T.107, I.108, H.134, R.136, D.176, E.180, F.247, P.286, W.290, H.396 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:T.43, B:T.43, B:T.43, B:G.103, B:T.107, B:T.107, B:T.107, B:R.136, B:D.176, B:D.176, B:Y.255, B:W.290 Salt bridges: B:H.396 pi-Stacking: B:F.247 ATP.6: 17 residues within 4Å: Chain C: I.25, Y.42, T.43, L.45, G.103, G.105, K.106, T.107, I.108, H.134, R.136, D.176, E.180, F.247, P.286, W.290, H.396 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:T.43, C:T.43, C:G.103, C:K.106, C:T.107, C:T.107, C:T.107, C:R.136, C:D.176, C:D.176, C:W.290 Salt bridges: C:H.134, C:H.396 pi-Stacking: C:F.247 ATP.8: 14 residues within 4Å: Chain D: I.25, Y.42, T.43, L.45, G.103, G.105, T.107, I.108, D.176, E.180, F.247, P.286, W.290, H.396 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:T.43, D:T.43, D:T.43, D:G.103, D:T.107, D:T.107, D:T.107, D:D.176, D:E.180, D:Y.255, D:W.290 Salt bridges: D:H.396 ATP.10: 17 residues within 4Å: Chain E: I.25, Y.42, T.43, L.45, G.103, G.105, K.106, T.107, I.108, H.134, R.136, D.176, E.180, F.247, P.286, W.290, H.396 13 PLIP interactions: 13 interactions with chain E Hydrogen bonds: E:T.43, E:T.43, E:T.43, E:G.103, E:K.106, E:T.107, E:T.107, E:T.107, E:R.136, E:D.176, E:D.176, E:W.290 Salt bridges: E:H.396 ATP.12: 17 residues within 4Å: Chain F: I.25, Y.42, T.43, L.45, G.103, G.105, K.106, T.107, I.108, H.134, R.136, D.176, E.180, F.247, P.286, W.290, H.396 12 PLIP interactions: 12 interactions with chain F Hydrogen bonds: F:T.43, F:T.43, F:G.103, F:K.106, F:T.107, F:T.107, F:T.107, F:R.136, F:D.176, F:D.176, F:W.290 Salt bridges: F:H.396

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yu, X. et al., Cryo-EM structures of NLRP3 reveal its self-activation mechanism. Nat Commun (2024)

Release Date

2024-02-14

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

NACHT, LRR and PYD domains-containing protein 3

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