› 3gs8

X-ray diffraction
2.85Å resolution

An all-RNA hairpin ribozyme A38N1dA38 variant with a transition-state mimic substrate strand

Released:
DOI: 10.2210/pdb3gs8/pdb
PDB entry 3gs8 coloured by chain, front view.
PDB entry 3gs8 coloured by chain, side view.
PDB entry 3gs8 coloured by chain, top view.
Source organism: Synthetic construct
Primary publication:
Identification of an imino group indispensable for cleavage by a small ribozyme.
Spitale RC, Volpini R, Heller MG, Krucinska J, Cristalli G, Wedekind JE
J Am Chem Soc 131 6093-5 (2009)
PMID: 19354216

Function and Biology Details

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-196680 (preferred)
Entry contents:
4 distinct RNA molecules
Macromolecules (4 distinct):
RNA (5'-R(*UP*CP*CP*CP*AP*GP*UP*CP*CP*AP*CP*CP*GP*U)-3') Chain: A
Molecule details ›
Chain: A
Length: 14 nucleotides
Theoretical weight: 4.36 KDa
Source organism: Synthetic construct
Expression system: Not provided
RNA (5'-R(*CP*GP*GP*UP*GP*AP*GP*AP*AP*GP*GP*G)-3') Chain: B
Molecule details ›
Chain: B
Length: 12 nucleotides
Theoretical weight: 3.97 KDa
Source organism: Synthetic construct
Expression system: Not provided
RNA (5'-R(P*GP*GP*CP*AP*GP*AP*GP*AP*AP*AP*CP*AP*CP*AP*CP*GP*A)-3') Chain: C
Molecule details ›
Chain: C
Length: 17 nucleotides
Theoretical weight: 5.54 KDa
Source organism: Synthetic construct
Expression system: Not provided
RNA (5'-R(*UP*CP*GP*UP*GP*GP*UP*AP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C)-3') Chain: D
Molecule details ›
Chain: D
Length: 19 nucleotides
Theoretical weight: 5.99 KDa
Source organism: Synthetic construct
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand SO4 1 x SO4
Ligand S9L 1 x S9L
Ligand NCO 2 x NCO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RUH2R
Spacegroup: P6122
Unit cell:
a: 93.82Å b: 93.82Å c: 134.76Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.22 0.22 0.254
Expression system: Not provided

Quick links

Citations

4 review citations

The DNA and RNA sugar-phosphate backbone emerges as the key player. An overview of quantum-chemical, structural biology and simulation studies.
Šponer et al. (2012)
3 more