› 5k7d

X-ray diffraction
2.68Å resolution

The structure of native pistol ribozyme, bound to Iridium

Released:
DOI: 10.2210/pdb5k7d/pdb
PDB entry 5k7d coloured by chain, front view.
PDB entry 5k7d coloured by chain, side view.
PDB entry 5k7d coloured by chain, top view.
Source organism: synthetic construct
Primary publication:
Pistol ribozyme adopts a pseudoknot fold facilitating site-specific in-line cleavage.
Ren A, Vušurović N, Gebetsberger J, Gao P, Juen M, Kreutz C, Micura R, Patel DJ
Nat Chem Biol 12 702-8 (2016)
PMID: 27398999

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-113179 (preferred)
Entry contents:
2 distinct DNA/RNA hybrid molecules
Macromolecules (2 distinct):
RNA 47-MER Chain: A
Molecule details ›
Chain: A
Length: 47 nucleotides
Theoretical weight: 15.1 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA/RNA 11-MER Chain: B
Molecule details ›
Chain: B
Length: 11 nucleotides
Theoretical weight: 3.51 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand IRI 2 x IRI
Ligand MG 5 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P3221
Unit cell:
a: 56.573Å b: 56.573Å c: 88.297Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.19 0.19 0.24
Expression system: Not provided

Quick links

Citations

7 review citations

Structure-based mechanistic insights into catalysis by small self-cleaving ribozymes.
Ren et al. (2017)
6 more

2 mentions without citation

Pistol ribozyme adopts a pseudoknot fold facilitating site-specific in-line cleavage.
Ren et al. (2016)
1 more