› 1xpf

X-ray diffraction
2.3Å resolution

HIV-1 subtype A genomic RNA Dimerization Initiation Site

Released:
DOI: 10.2210/pdb1xpf/pdb
PDB entry 1xpf coloured by chain, front view.
PDB entry 1xpf coloured by chain, side view.
PDB entry 1xpf coloured by chain, top view.
Source organism: Synthetic construct
Primary publication:
Polymorphism of bulged-out residues in HIV-1 RNA DIS kissing complex and structure comparison with solution studies.
Ennifar E, Dumas P
J Mol Biol 356 771-82 (2006)
PMID: 16403527

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-196240 (preferred)
Entry contents:
1 distinct RNA molecule
Macromolecule:
5'-R(*CP*UP*UP*GP*CP*UP*GP*AP*GP*GP*UP*GP*CP*AP*CP*AP*CP*AP*GP*CP*AP*AP*G)-3' Chains: A, B
Molecule details ›
Chains: A, B
Length: 23 nucleotides
Theoretical weight: 7.4 KDa
Source organism: Synthetic construct
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand SO4 3 x SO4
Ligand MG 3 x MG
Ligand NA 1 x NA
Ligand SPM 1 x SPM
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-4
Spacegroup: C2221
Unit cell:
a: 28.364Å b: 120.209Å c: 97.969Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.243 0.243 0.246
Expression system: Not provided

Quick links

Citations

6 review citations

RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.
Šponer et al. (2018)
5 more

10 mentions without citation

Role of long interspersed nuclear element-1 in the regulation of chromatin landscapes and genome dynamics.
Ramos et al. (2021)
9 more