› 5f9f

X-ray diffraction
2.6Å resolution

Crystal structure of RIG-I helicase-RD in complex with 24-mer blunt-end hairpin RNA

Released:
DOI: 10.2210/pdb5f9f/pdb
PDB entry 5f9f coloured by chain, front view.
PDB entry 5f9f coloured by chain, side view.
PDB entry 5f9f coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis for m7G recognition and 2'-O-methyl discrimination in capped RNAs by the innate immune receptor RIG-I.
Devarkar SC, Wang C, Miller MT, Ramanathan A, Jiang F, Khan AG, Patel SS, Marcotrigiano J
Proc Natl Acad Sci U S A 113 596-601 (2016)
PMID: 26733676

Function and Biology Details

Reaction catalysed: 
ATP + H(2)O = ADP + phosphate
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dodecamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-132047 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
Antiviral innate immune response receptor RIG-I Chains: A, C, E, G, I, K
Molecule details ›
Chains: A, C, E, G, I, K
Length: 695 amino acids
Theoretical weight: 79.59 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O95786 (Residues: 232-925; Coverage: 75%)
Gene names: DDX58, RIGI
Sequence domains:
Structure domains:
RNA (5'-R(*GP*AP*AP*UP*AP*UP*AP*AP*UP*AP*GP*UP*GP*AP*UP*AP*UP*UP*AP*UP*AP*UP*UP*C)-3') Chains: B, D, F, H, J, L
Molecule details ›
Chains: B, D, F, H, J, L
Length: 24 nucleotides
Theoretical weight: 7.65 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand ZN 6 x ZN
Ligand MG 6 x MG
Ligand ETF 4 x ETF
Ligand BU3 13 x BU3
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: CHESS BEAMLINE F1
Spacegroup: P212121
Unit cell:
a: 111.524Å b: 174.252Å c: 308.288Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.206 0.203 0.259
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

80 review citations

DAMP-sensing receptors in sterile inflammation and inflammatory diseases.
Gong et al. (2020)
79 more

9 mentions without citation

When your cap matters: structural insights into self vs non-self recognition of 5' RNA by immunomodulatory host proteins.
Leung et al. (2016)
8 more