› 3c5d

X-ray diffraction
1.8Å resolution

Crystal structure of HIV-1 subtype F DIS extended duplex RNA bound to lividomycin

Released:
DOI: 10.2210/pdb3c5d/pdb
Model geometry
Fit model/data
PDB entry 3c5d coloured by chain, front view.
PDB entry 3c5d coloured by chain, side view.
PDB entry 3c5d coloured by chain, top view.
Source organism: Synthetic construct
Primary publication:
Binding of aminoglycoside antibiotics to the duplex form of the HIV-1 genomic RNA dimerization initiation site.
Freisz S, Lang K, Micura R, Dumas P, Ennifar E
Angew Chem Int Ed Engl 47 4110-3 (2008)
PMID: 18435520

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-113118 (preferred)
Entry contents:
1 distinct DNA/RNA hybrid molecule
Macromolecule:
'HIV-1 subtype F genomic RNA Chains: A, B
Molecule details ›
Chains: A, B
Length: 23 nucleotides
Theoretical weight: 7.46 KDa
Source organism: Synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand K 2 x K
Ligand LIV 2 x LIV
1 modified residue:
Ligand UMS 2 x UMS

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: ESRF BEAMLINE ID14-4
Spacegroup: C2
Unit cell:
a: 100.086Å b: 29.294Å c: 59.607Å
α: 90° β: 120.84° γ: 90°
R-values:
R R work R free
0.232 0.232 0.245
Expression system: Not provided

Quick links

Citations

7 review citations

Chemical RNA modifications for studies of RNA structure and dynamics.
Wachowius et al. (2010)
6 more

2 mentions without citation

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