› 1m9d

X-ray diffraction
1.9Å resolution

X-ray crystal structure of Cyclophilin A/HIV-1 CA N-terminal domain (1-146) O-type chimera Complex.

Released:
DOI: 10.2210/pdb1m9d/pdb
PDB entry 1m9d coloured by chain, front view.
PDB entry 1m9d coloured by chain, side view.
PDB entry 1m9d coloured by chain, top view.
Source organisms:
Primary publication:
Structural insights into the catalytic mechanism of cyclophilin A.
Howard BR, Vajdos FF, Li S, Sundquist WI, Hill CP
Nat Struct Biol 10 475-81 (2003)
PMID: 12730686

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 domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-146203 (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: 18.04 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P62937 (Residues: 1-165; Coverage: 100%)
Gene names: CYPA, PPIA
Sequence domains: Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD
Structure domains: Cyclophilin-like
Capsid protein p24 Chains: C, D
Molecule details ›
Chains: C, D
Length: 146 amino acids
Theoretical weight: 16.19 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P12497 (Residues: 133-278; 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: SSRL BEAMLINE BL9-1
Spacegroup: P21
Unit cell:
a: 38.9Å b: 109.3Å c: 67.7Å
α: 90° β: 99.7° γ: 90°
R-values:
R R work R free
0.17 0.163 0.232
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

11 review citations

Prolyl cis-trans isomerization as a molecular timer.
Lu et al. (2007)
10 more

4 mentions without citation

Inhibitors of peptidyl proline isomerases as antivirals in hepatitis C and other viruses.
Striker et al. (2014)
3 more