SMTL ID : 7jl3.1

Cryo-EM structure of RIG-I:dsRNA filament in complex with RIPLET PrySpry domain (trimer)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-mer

Ligands

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

ADP.1: 15 residues within 4Å: Chain A: F.38, K.39, R.41, P.62, T.63, G.64, C.65, G.66, K.67, T.68, F.69, D.502, R.529 Ligands: ALF.2, MG.3 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:K.39, A:K.39, A:R.41, A:R.41, A:P.62, A:G.64, A:C.65, A:G.66, A:K.67, A:T.68, A:D.502 Salt bridges: A:K.67, A:K.67, A:R.529, A:R.529 pi-Cation interactions: A:R.41 ADP.5: 15 residues within 4Å: Chain C: F.38, K.39, R.41, P.62, T.63, G.64, C.65, G.66, K.67, T.68, F.69, D.502, R.529 Ligands: ALF.6, MG.7 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:K.39, C:K.39, C:R.41, C:R.41, C:P.62, C:G.64, C:C.65, C:G.66, C:K.67, C:T.68, C:D.502 Salt bridges: C:K.67, C:K.67, C:R.529, C:R.529 pi-Cation interactions: C:R.41 ADP.9: 15 residues within 4Å: Chain E: F.38, K.39, R.41, P.62, T.63, G.64, C.65, G.66, K.67, T.68, F.69, D.502, R.529 Ligands: ALF.10, MG.11 16 PLIP interactions: 16 interactions with chain E Hydrogen bonds: E:K.39, E:K.39, E:R.41, E:R.41, E:P.62, E:G.64, E:C.65, E:G.66, E:K.67, E:T.68, E:D.502 Salt bridges: E:K.67, E:K.67, E:R.529, E:R.529 pi-Cation interactions: E:R.41

3 x ALF: TETRAFLUOROALUMINATE ION(Non-covalent)

ALF.2: 10 residues within 4Å: Chain A: T.63, K.67, E.170, A.207, G.500, Q.523, R.527, R.529 Ligands: ADP.1, MG.3 No protein-ligand interaction detected (PLIP) ALF.6: 10 residues within 4Å: Chain C: T.63, K.67, E.170, A.207, G.500, Q.523, R.527, R.529 Ligands: ADP.5, MG.7 No protein-ligand interaction detected (PLIP) ALF.10: 10 residues within 4Å: Chain E: T.63, K.67, E.170, A.207, G.500, Q.523, R.527, R.529 Ligands: ADP.9, MG.11 No protein-ligand interaction detected (PLIP)

3 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: E.170 Ligands: ADP.1, ALF.2 No protein-ligand interaction detected (PLIP) MG.7: 3 residues within 4Å: Chain C: E.170 Ligands: ADP.5, ALF.6 No protein-ligand interaction detected (PLIP) MG.11: 3 residues within 4Å: Chain E: E.170 Ligands: ADP.9, ALF.10 No protein-ligand interaction detected (PLIP)

3 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain A: C.607, C.610, C.661, C.666 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.607, A:C.610, A:C.661, A:C.666 ZN.8: 4 residues within 4Å: Chain C: C.607, C.610, C.661, C.666 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.607, C:C.610, C:C.661, C:C.666 ZN.12: 4 residues within 4Å: Chain E: C.607, C.610, C.661, C.666 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.607, E:C.610, E:C.661, E:C.666

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kato, K. et al., Structural analysis of RIG-I-like receptors reveals ancient rules of engagement between diverse RNA helicases and TRIM ubiquitin ligases. Mol.Cell (2021)

Release Date

2020-12-09

Peptides

Antiviral innate immune response receptor RIG-I: ACE
E3 ubiquitin-protein ligase RNF135: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

B
B

D
D

F
F

Antiviral innate immune response receptor RIG-I

E3 ubiquitin-protein ligase RNF135

Related Entries With Identical Sequence