› 2xv6

X-ray diffraction
1.89Å resolution

Crystal structure of the HIV-1 capsid protein C-terminal domain (146- 220) in complex with a camelid VHH.

Released:
DOI: 10.2210/pdb2xv6/pdb
PDB entry 2xv6 coloured by chain, front view.
PDB entry 2xv6 coloured by chain, side view.
PDB entry 2xv6 coloured by chain, top view.
Source organisms:
Entry authors: Igonet S, Vaney MC, Bartonova V, Helma J, Rothbauer U, Leonhardt H, Stura E, Krausslich H-G, Rey FA

Function and Biology Details

Reactions catalysed: 
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:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-210530 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Capsid protein p24 Chains: A, C
Molecule details ›
Chains: A, C
Length: 75 amino acids
Theoretical weight: 8.46 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P12497 (Residues: 278-352; Coverage: 5%)
Gene name: gag-pol
Sequence domains: Gag protein p24 C-terminal domain
Structure domains: Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A
CAMELID VHH 9 Chains: B, D
Molecule details ›
Chains: B, D
Length: 121 amino acids
Theoretical weight: 13.21 KDa
Source organism: Vicugna pacos
Expression system: Escherichia coli BL21(DE3)
Structure domains: Immunoglobulins

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: P21
Unit cell:
a: 34.451Å b: 60.118Å c: 96.662Å
α: 90° β: 99.7° γ: 90°
R-values:
R R work R free
0.176 0.175 0.195
Expression system: Escherichia coli BL21(DE3)

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