› 2ypk

X-ray diffraction
1.95Å resolution

Structural features underlying T-cell receptor sensitivity to concealed MHC class I micropolymorphisms

Released:
DOI: 10.2210/pdb2ypk/pdb
PDB entry 2ypk coloured by chain, front view.
PDB entry 2ypk coloured by chain, side view.
PDB entry 2ypk coloured by chain, top view.
Source organisms:
Primary publication:
Structural features underlying T-cell receptor sensitivity to concealed MHC class I micropolymorphisms.
Stewart-Jones GB, Simpson P, van der Merwe PA, Easterbrook P, McMichael AJ, Rowland-Jones SL, Jones EY, Gillespie GM
Proc Natl Acad Sci U S A 109 E3483-92 (2012)
PMID: 23161907

Function and Biology Details

Reactions catalysed: 
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.
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-135253 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
HLA class I histocompatibility antigen, B alpha chain Chain: A
Molecule details ›
Chain: A
Length: 274 amino acids
Theoretical weight: 31.51 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P01889 (Residues: 25-298; Coverage: 81%)
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 BL21(DE3)
UniProt:
  • Canonical: P61769 (Residues: 21-119; Coverage: 100%)
Gene names: B2M, CDABP0092, HDCMA22P
Sequence domains: Immunoglobulin C1-set domain
Structure domains: Immunoglobulins
Pr55Gag Chain: C
Molecule details ›
Chain: C
Length: 11 amino acids
Theoretical weight: 1.27 KDa
Source organism: Human immunodeficiency virus
Expression system: Not provided
UniProt:
  • Canonical: Q70XD7 (Residues: 162-172; Coverage: 1%)

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-2
Spacegroup: P212121
Unit cell:
a: 50.829Å b: 82.067Å c: 110.489Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.194 0.191 0.252
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

5 review citations

T cell antigen receptor recognition of antigen-presenting molecules.
Rossjohn et al. (2015)
4 more

4 mentions without citation

Key role of human leukocyte antigen in modulating human immunodeficiency virus progression: An overview of the possible applications.
Grifoni et al. (2015)
3 more