› 3zd7

X-ray diffraction
2.5Å resolution

Snapshot 3 of RIG-I scanning on RNA duplex

Released:
DOI: 10.2210/pdb3zd7/pdb
PDB entry 3zd7 coloured by chain, front view.
PDB entry 3zd7 coloured by chain, side view.
PDB entry 3zd7 coloured by chain, top view.
Source organisms:
Primary publication:
Defining the functional determinants for RNA surveillance by RIG-I.
Kohlway A, Luo D, Rawling DC, Ding SC, Pyle AM
EMBO Rep 14 772-9 (2013)
PMID: 23897087

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 trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-132022 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
Antiviral innate immune response receptor RIG-I Chain: A
Molecule details ›
Chain: A
Length: 696 amino acids
Theoretical weight: 79.71 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: O95786 (Residues: 230-925; Coverage: 75%)
Gene names: DDX58, RIGI
Sequence domains:
Structure domains:
RNA DUPLEX Chains: C, D
Molecule details ›
Chains: C, D
Length: 10 nucleotides
Theoretical weight: 3.21 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand ZN 1 x ZN
Ligand MG 1 x MG
Ligand ADP 1 x ADP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P212121
Unit cell:
a: 48.252Å b: 75.996Å c: 207.279Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.232 0.229 0.288
Expression system: Not provided

Quick links

Citations

22 review citations

Discriminating self from non-self in nucleic acid sensing.
Schlee et al. (2016)
21 more

4 mentions without citation

Host DDX Helicases as Possible SARS-CoV-2 Proviral Factors: A Structural Overview of Their Hijacking Through Multiple Viral Proteins.
Squeglia et al. (2020)
3 more