› 1p7q

X-ray diffraction
3.4Å resolution

Crystal Structure of HLA-A2 Bound to LIR-1, a Host and Viral MHC Receptor

Released:
DOI: 10.2210/pdb1p7q/pdb
PDB entry 1p7q coloured by chain, front view.
PDB entry 1p7q coloured by chain, side view.
PDB entry 1p7q coloured by chain, top view.
Source organisms:
Primary publication:
Crystal structure of HLA-A2 bound to LIR-1, a host and viral major histocompatibility complex receptor.
Willcox BE, Thomas LM, Bjorkman PJ
Nat Immunol 4 913-9 (2003)
PMID: 12897781

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 tetramer (preferred)
PDBe Complex ID:
PDB-CPX-137661 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
HLA class I histocompatibility antigen, A alpha chain Chain: A
Molecule details ›
Chain: A
Length: 276 amino acids
Theoretical weight: 31.95 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 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
p51 RT Chain: C
Molecule details ›
Chain: C
Length: 9 amino acids
Theoretical weight: 993 Da
Source organism: Human immunodeficiency virus type 1 (Z2/CDC-Z34 ISOLATE)
Expression system: Not provided
UniProt:
  • Canonical: P12499 (Residues: 897-905; Coverage: 1%)
Gene name: gag-pol
Leukocyte immunoglobulin-like receptor subfamily B member 1 Chain: D
Molecule details ›
Chain: D
Length: 197 amino acids
Theoretical weight: 22 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8NHL6 (Residues: 25-221; Coverage: 31%)
Gene names: ILT2, LILRB1, LIR1, MIR7
Sequence domains: Immunoglobulin domain
Structure domains: Immunoglobulins

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.3
Spacegroup: P3121
Unit cell:
a: 113.74Å b: 113.74Å c: 89.46Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.222 0.218 0.309
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

50 review citations

Macromolecular modeling with rosetta.
Das et al. (2008)
49 more

24 mentions without citation

Global dynamics of proteins: bridging between structure and function.
Bahar et al. (2010)
23 more