› 2d2l

X-ray diffraction
2.5Å resolution

Crystal Structure of a minimal, all-RNA hairpin ribozyme with a propyl linker (C3) at position U39

Released:
DOI: 10.2210/pdb2d2l/pdb
PDB entry 2d2l coloured by chain, front view.
PDB entry 2d2l coloured by chain, side view.
PDB entry 2d2l coloured by chain, top view.
Source organism: Synthetic construct
Primary publication:
Conformational heterogeneity at position U37 of an all-RNA hairpin ribozyme with implications for metal binding and the catalytic structure of the S-turn.
Alam S, Grum-Tokars V, Krucinska J, Kundracik ML, Wedekind JE
Biochemistry 44 14396-408 (2005)
PMID: 16262240

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-196331 (preferred)
Entry contents:
4 distinct RNA molecules
Macromolecules (4 distinct):
5'-R(*UP*CP*CP*CP*(A2M)P*GP*UP*CP*CP*AP*CP*CP*G)-3' Chain: A
Molecule details ›
Chain: A
Length: 13 nucleotides
Theoretical weight: 4.07 KDa
Source organism: Synthetic construct
Expression system: Not provided
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
5'-R(*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
5'-R(*UP*CP*GP*UP*GP*GP*UP*AP*(P1P)P*AP*UP*UP*AP*CP*CP*UP*GP*CP*C)-3' Chain: D
Molecule details ›
Chain: D
Length: 19 nucleotides
Theoretical weight: 5.82 KDa
Source organism: Synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand SO4 1 x SO4
Ligand NCO 3 x NCO
1 modified residue:
Ligand A2M 1 x A2M

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RUH2R
Spacegroup: P6122
Unit cell:
a: 93.2Å b: 93.2Å c: 122.19Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.226 0.226 0.249
Expression system: Not provided

Quick links

Citations

9 review citations

Comparative enzymology and structural biology of RNA self-cleavage.
Fedor MJ. (2009)
8 more

2 mentions without citation

Sequence dependent variations in RNA duplex are related to non-canonical hydrogen bond interactions in dinucleotide steps.
Kailasam et al. (2014)
1 more