PDBe 1e27

X-ray diffraction
2.2Å resolution

Nonstandard peptide binding of HLA-B*5101 complexed with HIV immunodominant epitope KM1(LPPVVAKEI)

Released:

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:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
HLA class I histocompatibility antigen, B-51 alpha chain Chain: A
Molecule details ›
Chain: A
Length: 276 amino acids
Theoretical weight: 32.05 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P18464 (Residues: 25-300; Coverage: 82%)
Gene names: HLA-B, HLAB
Sequence domains:
Structure domains:
Beta-2-microglobulin Chain: B
Molecule details ›
Chain: B
Length: 99 amino acids
Theoretical weight: 11.75 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
Integrase Chain: C
Molecule details ›
Chain: C
Length: 9 amino acids
Theoretical weight: 966 Da
Source organism: Human immunodeficiency virus 1
Expression system: Not provided
UniProt:
  • Canonical: P24740 (Residues: 1168-1176; Coverage: 1%)
Gene name: gag-pol

Ligands and Environments

No bound ligands

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SRS BEAMLINE PX9.6
Spacegroup: P212121
Unit cell:
a: 50.8Å b: 82.3Å c: 111Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.199 0.199 0.255
Expression systems:
  • Escherichia coli BL21
  • Escherichia coli
  • Not provided