› 7jl3

Electron Microscopy
4.2Å resolution

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

Released:
DOI: 10.2210/pdb7jl3/pdb
PDB entry 7jl3 coloured by chain, front view.
PDB entry 7jl3 coloured by chain, side view.
PDB entry 7jl3 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural analysis of RIG-I-like receptors reveals ancient rules of engagement between diverse RNA helicases and TRIM ubiquitin ligases.
Kato K, Ahmad S, Zhu Z, Young JM, Mu X, Park S, Malik HS, Hur S
Mol Cell 81 599-613.e8 (2021)
PMID: 33373584
Related structures: EMD-22371

Function and Biology Details

Reactions catalysed: 
ATP + H(2)O = ADP + phosphate
S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero octamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-523096 (preferred)
Entry contents:
2 distinct polypeptide molecules
2 distinct RNA molecules
Macromolecules (4 distinct):
Antiviral innate immune response receptor RIG-I Chains: A, C, E
Molecule details ›
Chains: A, C, E
Length: 722 amino acids
Theoretical weight: 82.72 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O95786 (Residues: 204-925; Coverage: 78%)
Gene names: DDX58, RIGI
Sequence domains:
E3 ubiquitin-protein ligase RNF135 Chains: B, D, F
Molecule details ›
Chains: B, D, F
Length: 184 amino acids
Theoretical weight: 21.02 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8IUD6 (Residues: 249-432; Coverage: 43%)
Gene names: L13, RNF135
Sequence domains: SPRY domain
dsRNA strand1 Chain: X
Molecule details ›
Chain: X
Length: 42 nucleotides
Theoretical weight: 13.55 KDa
dsRNA strand 2 Chain: Y
Molecule details ›
Chain: Y
Length: 42 nucleotides
Theoretical weight: 13.36 KDa

Ligands and Environments

4 bound ligands:
Ligand ADP 3 x ADP
Ligand ALF 3 x ALF
Ligand MG 3 x MG
Ligand ZN 3 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 4.2Å
Relevant EMDB volumes: EMD-22371
Expression system: Escherichia coli

Quick links

Citations

10 review citations

Pattern recognition receptors in health and diseases.
Li et al. (2021)
9 more

1 mention without citation

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