› 2oj3

X-ray diffraction
2.9Å resolution

Hepatitis Delta Virus ribozyme precursor structure, with C75U mutation, bound to Tl+ and cobalt hexammine (Co(NH3)63+)

Released:
DOI: 10.2210/pdb2oj3/pdb
PDB entry 2oj3 coloured by chain, front view.
PDB entry 2oj3 coloured by chain, side view.
PDB entry 2oj3 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural roles of monovalent cations in the HDV ribozyme.
Ke A, Ding F, Batchelor JD, Doudna JA
Structure 15 281-7 (2007)
PMID: 17355864

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-140479 (preferred)
Entry contents:
1 distinct polypeptide molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
U1 small nuclear ribonucleoprotein A Chain: A
Molecule details ›
Chain: A
Length: 100 amino acids
Theoretical weight: 11.5 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P09012 (Residues: 2-100; Coverage: 35%)
Gene name: SNRPA
Sequence domains: RNA recognition motif
Structure domains: Alpha-Beta Plaits
HDV RIBOZYME Chain: B
Molecule details ›
Chain: B
Length: 75 nucleotides
Theoretical weight: 24.16 KDa
Source organism: Homo sapiens
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand NCO 2 x NCO
Ligand TL 9 x TL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.2.1
Spacegroup: R32
Unit cell:
a: 108.607Å b: 108.607Å c: 188.211Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.228 0.228 0.263
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

9 review citations

Ribozymes, riboswitches and beyond: regulation of gene expression without proteins.
Serganov et al. (2007)
8 more

2 mentions without citation

Mechanistic strategies in the HDV ribozyme: chelated and diffuse metal ion interactions and active site protonation.
Veeraraghavan et al. (2011)
1 more