SMTL ID : 7jl2.1

Cryo-EM structure of MDA5-dsRNA filament in complex with TRIM65 PSpry domain (Trimer)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-mer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain C: C.621, C.624, C.676, C.678 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.621, C:C.624, C:C.676, C:C.678 ZN.5: 4 residues within 4Å: Chain E: C.621, C.624, C.676, C.678 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.621, E:C.624, E:C.676, E:C.678 ZN.9: 4 residues within 4Å: Chain G: C.621, C.624, C.676, C.678 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.621, G:C.624, G:C.676, G:C.678

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

ADP.2: 15 residues within 4Å: Chain C: Q.21, R.23, Q.26, T.45, G.46, S.47, G.48, K.49, T.50, R.51, D.511, K.513, R.538 Ligands: ALF.3, MG.4 20 PLIP interactions: 20 interactions with chain C Hydrogen bonds: C:Q.21, C:R.23, C:R.23, C:Q.26, C:G.46, C:S.47, C:G.48, C:K.49, C:T.50, C:R.51, C:R.51, C:D.511, C:D.511, C:K.513 Salt bridges: C:K.49, C:R.538, C:R.538 pi-Cation interactions: C:R.23, C:R.51, C:R.51 ADP.6: 15 residues within 4Å: Chain E: Q.21, R.23, Q.26, T.45, G.46, S.47, G.48, K.49, T.50, R.51, D.511, K.513, R.538 Ligands: ALF.7, MG.8 20 PLIP interactions: 20 interactions with chain E Hydrogen bonds: E:Q.21, E:R.23, E:R.23, E:Q.26, E:G.46, E:S.47, E:G.48, E:K.49, E:T.50, E:R.51, E:R.51, E:D.511, E:D.511, E:K.513 Salt bridges: E:K.49, E:R.538, E:R.538 pi-Cation interactions: E:R.23, E:R.51, E:R.51 ADP.10: 15 residues within 4Å: Chain G: Q.21, R.23, Q.26, T.45, G.46, S.47, G.48, K.49, T.50, R.51, D.511, K.513, R.538 Ligands: ALF.11, MG.12 20 PLIP interactions: 20 interactions with chain G Hydrogen bonds: G:Q.21, G:R.23, G:R.23, G:Q.26, G:G.46, G:S.47, G:G.48, G:K.49, G:T.50, G:R.51, G:R.51, G:D.511, G:D.511, G:K.513 Salt bridges: G:K.49, G:R.538, G:R.538 pi-Cation interactions: G:R.23, G:R.51, G:R.51

3 x ALF: TETRAFLUOROALUMINATE ION(Non-covalent)

ALF.3: 8 residues within 4Å: Chain C: T.45, K.49, G.509, Q.532, R.536, R.538 Ligands: ADP.2, MG.4 No protein-ligand interaction detected (PLIP) ALF.7: 8 residues within 4Å: Chain E: T.45, K.49, G.509, Q.532, R.536, R.538 Ligands: ADP.6, MG.8 No protein-ligand interaction detected (PLIP) ALF.11: 8 residues within 4Å: Chain G: T.45, K.49, G.509, Q.532, R.536, R.538 Ligands: ADP.10, MG.12 No protein-ligand interaction detected (PLIP)

3 x MG: MAGNESIUM ION(Non-functional Binders)

MG.4: 2 residues within 4Å: Ligands: ADP.2, ALF.3 No protein-ligand interaction detected (PLIP) MG.8: 2 residues within 4Å: Ligands: ADP.6, ALF.7 No protein-ligand interaction detected (PLIP) MG.12: 2 residues within 4Å: Ligands: ADP.10, ALF.11 No protein-ligand interaction detected (PLIP)

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

Interferon-induced helicase C domain-containing protein 1: CEG
Tripartite motif-containing protein 65: DFH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

E
C

G
E

D
B

F
D

H
F

Interferon-induced helicase C domain-containing protein 1

Tripartite motif-containing protein 65

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