SMTL ID : 7vtp.1

Cryo-EM structure of PYD-deleted human NLRP3 hexamer

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

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

ADP.1: 16 residues within 4Å: Chain A: R.62, Y.63, T.64, A.122, G.124, I.125, G.126, K.127, T.128, I.129, F.268, Y.276, P.307, L.308, W.311, H.417 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:T.64, A:T.64, A:T.64, A:G.124, A:I.125, A:G.126, A:K.127, A:T.128, A:T.128, A:I.129, A:Y.276 Salt bridges: A:K.127, A:H.417, A:H.417 pi-Stacking: A:F.268 ADP.3: 15 residues within 4Å: Chain B: R.62, Y.63, T.64, A.122, G.124, I.125, G.126, K.127, T.128, I.129, F.268, Y.276, P.307, W.311, H.417 15 PLIP interactions: 15 interactions with chain B Hydrogen bonds: B:T.64, B:T.64, B:T.64, B:G.124, B:I.125, B:G.126, B:K.127, B:T.128, B:T.128, B:I.129, B:Y.276 Salt bridges: B:K.127, B:H.417, B:H.417 pi-Stacking: B:F.268 ADP.5: 16 residues within 4Å: Chain C: R.62, Y.63, T.64, A.122, A.123, G.124, I.125, G.126, K.127, T.128, I.129, F.268, Y.276, P.307, W.311, H.417 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:T.64, C:T.64, C:T.64, C:G.124, C:I.125, C:G.126, C:K.127, C:T.128, C:T.128, C:I.129, C:Y.276 Salt bridges: C:K.127, C:H.417, C:H.417 pi-Stacking: C:F.268 ADP.7: 16 residues within 4Å: Chain D: R.62, Y.63, T.64, A.122, G.124, I.125, G.126, K.127, T.128, I.129, F.268, Y.276, P.307, L.308, W.311, H.417 14 PLIP interactions: 14 interactions with chain D Hydrogen bonds: D:T.64, D:T.64, D:G.124, D:I.125, D:G.126, D:K.127, D:T.128, D:T.128, D:T.128, D:I.129 Salt bridges: D:K.127, D:H.417, D:H.417 pi-Stacking: D:F.268 ADP.9: 15 residues within 4Å: Chain E: R.62, Y.63, T.64, A.122, G.124, I.125, G.126, K.127, T.128, I.129, F.268, Y.276, P.307, W.311, H.417 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:T.64, E:T.64, E:G.124, E:I.125, E:G.126, E:K.127, E:T.128, E:T.128, E:T.128, E:I.129 Salt bridges: E:K.127, E:H.417, E:H.417 pi-Stacking: E:F.268 ADP.11: 16 residues within 4Å: Chain F: R.62, Y.63, T.64, A.122, A.123, G.124, I.125, G.126, K.127, T.128, I.129, F.268, Y.276, P.307, W.311, H.417 14 PLIP interactions: 14 interactions with chain F Hydrogen bonds: F:T.64, F:T.64, F:G.124, F:I.125, F:G.126, F:K.127, F:T.128, F:T.128, F:T.128, F:I.129 Salt bridges: F:K.127, F:H.417, F:H.417 pi-Stacking: F:F.268

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.2: 13 residues within 4Å: Chain A: A.122, A.123, R.246, P.247, I.306, V.309, T.334, Y.338, F.470, R.473, E.524, Y.527, M.556 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:A.123, A:I.306, A:V.309, A:T.334, A:F.470, A:E.524, A:Y.527, A:Y.527 Hydrogen bonds: A:A.123, A:A.123, A:R.473, A:R.473, A:Y.527 pi-Cation interactions: A:R.473 7YN.4: 12 residues within 4Å: Chain B: A.122, A.123, R.246, I.306, V.309, T.334, Y.338, F.470, R.473, E.524, Y.527, M.556 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:A.123, B:I.306, B:V.309, B:T.334, B:F.470, B:E.524, B:Y.527 Hydrogen bonds: B:A.123, B:A.123, B:R.246, B:R.473, B:R.473, B:Y.527 7YN.6: 13 residues within 4Å: Chain C: A.122, A.123, R.246, P.247, I.306, V.309, T.334, Y.338, F.470, R.473, E.524, Y.527, M.556 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:A.123, C:I.306, C:V.309, C:T.334, C:F.470, C:Y.527 Hydrogen bonds: C:A.123, C:A.123, C:R.246, C:R.473, C:R.473, C:Y.527 pi-Cation interactions: C:R.473 7YN.8: 13 residues within 4Å: Chain D: A.122, A.123, R.246, P.247, I.306, V.309, T.334, Y.338, F.470, R.473, E.524, Y.527, M.556 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:A.123, D:I.306, D:V.309, D:T.334, D:F.470, D:E.524, D:Y.527, D:Y.527 Hydrogen bonds: D:A.123, D:A.123, D:R.473, D:R.473 pi-Cation interactions: D:R.473 7YN.10: 12 residues within 4Å: Chain E: A.122, A.123, R.246, I.306, V.309, T.334, Y.338, F.470, R.473, E.524, Y.527, M.556 12 PLIP interactions: 12 interactions with chain E Hydrophobic interactions: E:I.306, E:V.309, E:T.334, E:F.470, E:E.524, E:Y.527 Hydrogen bonds: E:A.123, E:A.123, E:R.246, E:R.473, E:R.473, E:Y.527 7YN.12: 12 residues within 4Å: Chain F: A.122, A.123, R.246, I.306, V.309, T.334, Y.338, F.470, R.473, E.524, Y.527, M.556 14 PLIP interactions: 14 interactions with chain F Hydrophobic interactions: F:A.123, F:I.306, F:V.309, F:T.334, F:F.470, F:E.524, F:Y.527 Hydrogen bonds: F:A.123, F:A.123, F:R.246, F:R.473, F:R.473, F:Y.527 pi-Cation interactions: F:R.473

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: 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