› 2oj0

X-ray diffraction
2.6Å resolution

Crystal structure of the duplex form of the HIV-1(LAI) RNA dimerization initiation site MN soaked

Released:
DOI: 10.2210/pdb2oj0/pdb
PDB entry 2oj0 coloured by chain, front view.
PDB entry 2oj0 coloured by chain, side view.
PDB entry 2oj0 coloured by chain, top view.
Source organism: Synthetic construct
Primary publication:
Cation-dependent cleavage of the duplex form of the subtype-B HIV-1 RNA dimerization initiation site.
Ennifar E, Walter P, Dumas P
Nucleic Acids Res 38 5807-16 (2010)
PMID: 20460458

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-196554 (preferred)
Entry contents:
1 distinct RNA molecule
Macromolecule:
5'-R(*CP*UP*UP*GP*CP*UP*GP*AP*AP*GP*CP*GP*CP*GP*CP*AP*CP*GP*GP*CP*AP*AP*G)-3' Chains: A, B
Molecule details ›
Chains: A, B
Length: 23 nucleotides
Theoretical weight: 7.42 KDa
Source organism: Synthetic construct
Expression system: Not provided

Ligands and Environments

3 bound ligands:
Ligand K 5 x K
Ligand MN 3 x MN
Ligand NA 3 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE BM30A
Spacegroup: P21212
Unit cell:
a: 42.538Å b: 47.834Å c: 58.681Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.2 0.2 0.23
Expression system: Not provided

Quick links

Citations

2 review citations

Interaction of Na+, K+, Mg2+ and Ca2+ counter cations with RNA.
Kolev et al. (2018)
1 more

2 mentions without citation

Structural and computational studies of HIV-1 RNA.
Levintov et al. (2024)
1 more