› 5v5m

X-ray diffraction
2.88Å resolution

Crystal structure of HLA-B*5701 complex with HIV-1 gag derived peptide TW10

Released:
DOI: 10.2210/pdb5v5m/pdb
PDB entry 5v5m coloured by chain, front view.
PDB entry 5v5m coloured by chain, side view.
PDB entry 5v5m coloured by chain, top view.
Source organisms:
Primary publication:
Crystal structure of HLA-B*5801 with a TW10 HIV Gag epitope reveals a novel mode of peptide presentation.
Li X, Lamothe PA, Walker BD, Wang JH
Cell Mol Immunol 14 631-634 (2017)
PMID: 28552904

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 analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-135136 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
HLA class I histocompatibility antigen, B alpha chain Chains: A, C
Molecule details ›
Chains: A, C
Length: 278 amino acids
Theoretical weight: 32.01 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P01889 (Residues: 25-300; Coverage: 82%)
Gene names: HLA-B, HLAB
Sequence domains:
Structure domains:
Beta-2-microglobulin Chains: B, D
Molecule details ›
Chains: B, D
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
Capsid protein p24 Chains: E, F
Molecule details ›
Chains: E, F
Length: 10 amino acids
Theoretical weight: 1.16 KDa
Source organism: Human immunodeficiency virus 1
Expression system: Not provided
UniProt:
  • Canonical: P03366 (Residues: 240-249; 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: APS BEAMLINE 19-ID
Spacegroup: P212121
Unit cell:
a: 69.674Å b: 82.622Å c: 157.779Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.201 0.198 0.244
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

5 review citations

Predicting Antigen Presentation-What Could We Learn From a Million Peptides?
Gfeller et al. (2018)
4 more

1 mention without citation

Protective HLA-B57: T cell and natural killer cell recognition in HIV infection.
Lobos et al. (2022)