› 5ed1

X-ray diffraction
2.77Å resolution

Human Adenosine Deaminase Acting on dsRNA (ADAR2) mutant E488Q bound to dsRNA sequence derived from S. cerevisiae BDF2 gene

Released:
DOI: 10.2210/pdb5ed1/pdb
PDB entry 5ed1 coloured by chain, front view.
PDB entry 5ed1 coloured by chain, side view.
PDB entry 5ed1 coloured by chain, top view.
Source organisms:
Primary publication:
Structures of human ADAR2 bound to dsRNA reveal base-flipping mechanism and basis for site selectivity.
Matthews MM, Thomas JM, Zheng Y, Tran K, Phelps KJ, Scott AI, Havel J, Fisher AJ, Beal PA
Nat Struct Mol Biol 23 426-33 (2016)
PMID: 27065196

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

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-160292 (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 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(*UP*UP*CP*CP*CP*CP*AP*CP*AP*UP*UP*(8AZ)P*GP*AP*CP*GP*UP*UP*CP*AP*GP*UP*C)-3') Chain: B
Molecule details ›
Chain: B
Length: 23 nucleotides
Theoretical weight: 7.23 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Not provided
RNA (5'-R(*GP*AP*CP*UP*GP*AP*AP*CP*GP*AP*CP*CP*AP*AP*UP*GP*UP*GP*GP*GP*GP*AP*A)-3') Chain: C
Molecule details ›
Chain: C
Length: 23 nucleotides
Theoretical weight: 7.49 KDa
Source organism: Saccharomyces cerevisiae
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: APS BEAMLINE 24-ID-C
Spacegroup: P212121
Unit cell:
a: 82.362Å b: 107.498Å c: 121.097Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.166 0.163 0.223
Expression systems:
  • Saccharomyces cerevisiae
  • Not provided

Quick links

Citations

32 review citations

Base editing: precision chemistry on the genome and transcriptome of living cells.
Rees et al. (2018)
31 more

12 mentions without citation

From Antisense RNA to RNA Modification: Therapeutic Potential of RNA-Based Technologies.
Adachi et al. (2021)
11 more