PDBe 2x4u

X-ray diffraction
2.1Å resolution

Crystal structure of MHC CLass I HLA-A2.1 bound to HIV-1 Peptide RT468-476

Released:
Primary publication:
UV-induced ligand exchange in MHC class I protein crystals.
J. Am. Chem. Soc. 131 12298-304 (2009)
PMID: 19655750

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:
Cellular component:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
HLA class I histocompatibility antigen, A-2 alpha chain Chains: A, D
Molecule details ›
Chains: A, D
Length: 275 amino acids
Theoretical weight: 31.85 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P01892 (Residues: 25-299; Coverage: 81%)
Gene names: HLA-A, HLAA
Sequence domains:
Structure domains:
Beta-2-microglobulin Chains: B, E
Molecule details ›
Chains: B, E
Length: 100 amino acids
Theoretical weight: 11.88 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P61769 (Residues: 21-119; Coverage: 100%)
Gene names: B2M, CDABP0092, HDCMA22P
Sequence domains: Immunoglobulin C1-set domain
Structure domains: Immunoglobulins
p51 RT Chains: C, F
Molecule details ›
Chains: C, F
Length: 9 amino acids
Theoretical weight: 993 Da
Source organism: Human immunodeficiency virus 1
Expression system: Not provided
UniProt:
  • Canonical: P03366 (Residues: 908-916; Coverage: 1%)
Gene name: gag-pol

Ligands and Environments

2 bound ligands:

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-1
Spacegroup: P21
Unit cell:
a: 62.215Å b: 82.774Å c: 79.655Å
α: 90° β: 90.76° γ: 90°
R-values:
R R work R free
0.179 0.176 0.234
Expression systems:
  • Escherichia coli BL21(DE3)
  • Escherichia coli
  • Not provided