› 1pjg

X-ray diffraction
1.15Å resolution

RNA/DNA Hybrid Decamer of CAAAGAAAAG/CTTTTCTTTG

Released:
DOI: 10.2210/pdb1pjg/pdb
PDB entry 1pjg coloured by chain, front view.
PDB entry 1pjg coloured by chain, side view.
PDB entry 1pjg coloured by chain, top view.
Source organism: Synthetic construct
Primary publication:
An unusual sugar conformation in the structure of an RNA/DNA decamer of the polypurine tract may affect recognition by RNase H.
Kopka ML, Lavelle L, Han GW, Ng HL, Dickerson RE
J Mol Biol 334 653-65 (2003)
PMID: 14636594

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
PDBe Complex ID:
PDB-CPX-114390 (preferred)
Entry contents:
1 distinct DNA molecule
1 distinct RNA molecule
Macromolecules (2 distinct):
5'-D(*CP*TP*TP*TP*TP*CP*TP*TP*TP*G)-3' Chain: B
Molecule details ›
Chain: B
Length: 10 nucleotides
Theoretical weight: 2.99 KDa
Source organism: Synthetic construct
Expression system: Not provided
5'-R(*CP*AP*AP*AP*GP*AP*AP*AP*AP*G)-3' Chain: A
Molecule details ›
Chain: A
Length: 10 nucleotides
Theoretical weight: 3.26 KDa
Source organism: Synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand CA 4 x CA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X8C
Spacegroup: P212121
Unit cell:
a: 25.701Å b: 41.073Å c: 46.116Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.132 0.132 0.163
Expression system: Not provided

Quick links

Citations

3 review citations

RNase H activity: structure, specificity, and function in reverse transcription.
Schultz et al. (2008)
2 more

1 mention without citation

Molecular Dynamics Study of the Hybridization between RNA and Modified Oligonucleotides.
Jing et al. (2019)