› 6d06

X-ray diffraction
2.55Å resolution

Human ADAR2d E488Y mutant complexed with dsRNA containing an abasic site opposite the edited base

Released:
DOI: 10.2210/pdb6d06/pdb
PDB entry 6d06 coloured by chain, front view.
PDB entry 6d06 coloured by chain, side view.
PDB entry 6d06 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
A Bump-Hole Approach for Directed RNA Editing.
Monteleone LR, Matthews MM, Palumbo CM, Thomas JM, Zheng Y, Chiang Y, Fisher AJ, Beal PA
Cell Chem Biol 26 269-277.e5 (2019)
PMID: 30581135

Function and Biology Details

Reaction catalysed: 
Adenine in double-stranded RNA + H(2)O = hypoxanthine in double-stranded RNA + NH(3)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assemblies composition:
hetero trimer (preferred)
monomeric
Assembly name:
PDBe Complex ID:
PDB-CPX-160291 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct RNA molecules
Macromolecules (3 distinct):
Double-stranded RNA-specific editase 1 Chains: A, D
Molecule details ›
Chains: A, D
Length: 403 amino acids
Theoretical weight: 45.04 KDa
Source organism: Homo sapiens
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P78563 (Residues: 299-741; Coverage: 54%)
Gene names: ADAR2, ADARB1, DRADA2, RED1
Sequence domains: Adenosine-deaminase (editase) domain
RNA (5'-R(*GP*CP*UP*CP*GP*CP*GP*AP*UP*GP*CP*UP*(8AZ)P*GP*AP*GP*GP*GP*CP*UP*CP*UP*G)-3') Chain: B
Molecule details ›
Chain: B
Length: 23 nucleotides
Theoretical weight: 7.42 KDa
Source organism: Homo sapiens
Expression system: Not provided
RNA (5'-R(*CP*AP*GP*AP*GP*CP*CP*CP*CP*CP*NP*AP*GP*CP*AP*UP*CP*GP*CP*GP*AP*GP*C)-3') Chain: C
Molecule details ›
Chain: C
Length: 23 nucleotides
Theoretical weight: 7.23 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand IHP 2 x IHP
Ligand ZN 2 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL12-2
Spacegroup: C2
Unit cell:
a: 174.68Å b: 63.44Å c: 132.06Å
α: 90° β: 126.64° γ: 90°
R-values:
R R work R free
0.193 0.19 0.255
Expression systems:
  • Saccharomyces cerevisiae
  • Not provided

Quick links

Citations

5 review citations

Off-Target Editing by CRISPR-Guided DNA Base Editors.
Park et al. (2019)
4 more

2 mentions without citation

A Bump-Hole Approach for Directed RNA Editing.
Monteleone et al. (2019)
1 more