PDBe 3p0a

X-ray diffraction
5.95Å resolution

X-ray structure of pentameric HIV-1 CA

Primary publication:
Atomic-level modelling of the HIV capsid.
OpenAccess logo Nature 469 424-7 (2011)
PMID: 21248851

Function and Biology Details

Reactions catalysed:
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.
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Specific for a P1 residue that is hydrophobic, and P1' variable, but often Pro.
3'-end directed exonucleolytic cleavage of viral RNA-DNA hybrid
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
homo pentamer (preferred)
Entry contents:
1 distinct polypeptide molecule
Capsid protein p24 Chains: A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T
Molecule details ›
Chains: A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T
Length: 231 amino acids
Theoretical weight: 25.42 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Escherichia coli
  • Canonical: P12497 (Residues: 133-363; Coverage: 16%)
  • Canonical: Q72497 (Residues: 133-363; Coverage: 46%)
  • nullnull
Gene names: gag, gag-pol
Sequence domains: gag gene protein p24 (core nucleocapsid protein)

Ligands and Environments

No bound ligands

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P1
Unit cell:
a: 86.794Å b: 122.128Å c: 149.304Å
α: 74.41° β: 74.36° γ: 81.48°
R R work R free
0.299 0.297 0.316
Expression system: Escherichia coli