› 4dge

X-ray diffraction
2.2Å resolution

TRIMCyp cyclophilin domain from Macaca mulatta: H70C mutant, HIV-1 CA(O-loop) complex

Released:
DOI: 10.2210/pdb4dge/pdb
PDB entry 4dge coloured by chain, front view.
PDB entry 4dge coloured by chain, side view.
PDB entry 4dge coloured by chain, top view.
Source organisms:
Primary publication:
Diverse HIV viruses are targeted by a conformationally dynamic antiviral.
Caines ME, Bichel K, Price AJ, McEwan WA, Towers GJ, Willett BJ, Freund SM, James LC
Nat Struct Mol Biol 19 411-6 (2012)
PMID: 22407016

Function and Biology Details

Reactions catalysed: 
Peptidylproline (omega=180) = peptidylproline (omega=0)
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid
Endohydrolysis of RNA in RNA/DNA hybrids. Three different cleavage modes: 1. sequence-specific internal cleavage of RNA. Human immunodeficiency virus type 1 and Moloney murine leukemia virus enzymes prefer to cleave the RNA strand one nucleotide away from the RNA-DNA junction. 2. RNA 5'-end directed cleavage 13-19 nucleotides from the RNA end. 3. DNA 3'-end directed cleavage 15-20 nucleotides away from the primer terminus.
Specific for a P1 residue that is hydrophobic, and P1' variable, but often Pro.
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-146204 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Peptidyl-prolyl cis-trans isomerase A Chains: A, B
Molecule details ›
Chains: A, B
Length: 165 amino acids
Theoretical weight: 17.98 KDa
Source organism: Macaca mulatta
Expression system: Escherichia coli
UniProt:
  • Canonical: P62940 (Residues: 1-165; Coverage: 100%)
Gene names: CYPA, PPIA
Sequence domains: Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD
Structure domains: Cyclophilin-like
Matrix protein p17 Chains: C, D
Molecule details ›
Chains: C, D
Length: 146 amino acids
Theoretical weight: 16.18 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Escherichia coli
UniProt:
  • Canonical: P12497 (Residues: 132-277; Coverage: 10%)
Gene name: gag-pol
Structure domains: Human Immunodeficiency Virus Type 1 Capsid Protein

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-E+ SUPERBRIGHT
Spacegroup: P1
Unit cell:
a: 39.07Å b: 59.71Å c: 70.47Å
α: 65.08° β: 83.87° γ: 79.65°
R-values:
R R work R free
0.189 0.186 0.255
Expression system: Escherichia coli

Quick links

Citations

7 review citations

Cellular self-defense: how cell-autonomous immunity protects against pathogens.
Randow et al. (2013)
6 more

1 mention without citation

Target-Based Small Molecule Drug Discovery for Colorectal Cancer: A Review of Molecular Pathways and In Silico Studies.
Moshawih et al. (2022)