› 1q94

X-ray diffraction
2.4Å resolution

Structures of HLA-A*1101 in complex with immunodominant nonamer and decamer HIV-1 epitopes clearly reveal the presence of a middle anchor residue

Released:
DOI: 10.2210/pdb1q94/pdb
PDB entry 1q94 coloured by chain, front view.
PDB entry 1q94 coloured by chain, side view.
PDB entry 1q94 coloured by chain, top view.
Source organisms:
Primary publication:
Structures of HLA-A*1101 complexed with immunodominant nonamer and decamer HIV-1 epitopes clearly reveal the presence of a middle, secondary anchor residue.
Li L, Bouvier M
J Immunol 172 6175-84 (2004)
PMID: 15128805

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:
Biological process:
Cellular component:
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-137660 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
HLA class I histocompatibility antigen, A alpha chain Chains: A, D
Molecule details ›
Chains: A, D
Length: 275 amino acids
Theoretical weight: 31.86 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P04439 (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: 1.01 KDa
Source organism: Human immunodeficiency virus type 1 (Z2/CDC-Z34 ISOLATE)
Expression system: Not provided
UniProt:
  • Canonical: P12499 (Residues: 746-754; 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: CHESS BEAMLINE F1
Spacegroup: P1
Unit cell:
a: 45.4Å b: 46.4Å c: 124.3Å
α: 91.5° β: 97.9° γ: 114.8°
R-values:
R R work R free
0.234 0.232 0.272
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

2 review citations

Revival of the identification of cytotoxic T-lymphocyte epitopes for immunological diagnosis, therapy and vaccine development.
Liu et al. (2011)
1 more

14 mentions without citation

Crystal structure of swine major histocompatibility complex class I SLA-1 0401 and identification of 2009 pandemic swine-origin influenza A H1N1 virus cytotoxic T lymphocyte epitope peptides.
Zhang et al. (2011)
13 more