› 9d5k

X-ray diffraction
2.7Å resolution

Human Adenosine Deaminase Acting on dsRNA (ADAR2-RD) bound to dsRNA containing an expanded cytidine analog at the -1 position of the guide strand

Released:
DOI: 10.2210/pdb9d5k/pdb
PDB entry 9d5k coloured by chain, front view.
PDB entry 9d5k coloured by chain, side view.
PDB entry 9d5k coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Nucleoside Analogs in ADAR Guide Strands Enable Editing at 5'-G
Manjunath A, Cheng J, Campbell KB, Jacobsen CS, Mendoza HG, Bierbaum L, Jauregui-Matos V, Doherty EE, Fisher AJ, Beal PA
Biomolecules 14 (2024)
PMID: 39456162

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-505910 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
1 distinct DNA/RNA hybrid molecule
Macromolecules (3 distinct):
Double-stranded RNA-specific editase 1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 487 amino acids
Theoretical weight: 53.93 KDa
Source organism: Homo sapiens
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P78563 (Residues: 215-741; Coverage: 66%)
  • Best match: P78563-2 (Residues: 215-701)
Gene names: ADAR2, ADARB1, DRADA2, RED1
Sequence domains:
RNA Top Strand Chain: C
Molecule details ›
Chain: C
Length: 32 nucleotides
Theoretical weight: 10.36 KDa
Source organism: Homo sapiens
Expression system: Not provided
RNA Bottom Strand Chain: D
Molecule details ›
Chain: D
Length: 32 nucleotides
Theoretical weight: 10.24 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand IHP 2 x IHP
Ligand ZN 2 x ZN
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL12-1
Spacegroup: C2
Unit cell:
a: 174.775Å b: 63.112Å c: 141.064Å
α: 90° β: 118.538° γ: 90°
R-values:
R R work R free
0.223 0.221 0.268
Expression systems:
  • Saccharomyces cerevisiae
  • Not provided

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