› 7t6i

X-ray diffraction
2.3Å resolution

Crystal structure of HLA-DP1 in complex with pp65 peptide in reverse orientation

Released:
DOI: 10.2210/pdb7t6i/pdb
PDB entry 7t6i coloured by chain, front view.
PDB entry 7t6i coloured by chain, side view.
PDB entry 7t6i coloured by chain, top view.
Source organisms:
Primary publication:
Human T cells recognize HLA-DP-bound peptides in two orientations.
Klobuch S, Lim JJ, van Balen P, Kester MGD, de Klerk W, de Ru AH, Pothast CR, Jedema I, Drijfhout JW, Rossjohn J, Reid HH, van Veelen PA, Falkenburg JHF, Heemskerk MHM
Proc Natl Acad Sci U S A 119 e2214331119 (2022)
PMID: 36442096

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-139161 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Ig-like domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 183 amino acids
Theoretical weight: 21.02 KDa
Source organism: Homo sapiens
Expression system: Insect expression vector pBlueBacmsGCA1His
UniProt:
  • Canonical: Q95HB9 (Residues: 32-211; Coverage: 79%)
Gene name: HLA-DPA1
Sequence domains:
Ig-like domain-containing protein Chain: B
Molecule details ›
Chain: B
Length: 191 amino acids
Theoretical weight: 22.17 KDa
Source organism: Homo sapiens
Expression system: Insect expression vector pBlueBacmsGCB1His
UniProt:
  • Canonical: S6B6U4 (Residues: 30-217; Coverage: 82%)
Gene names: DPB1, HLA-DPB1
Sequence domains:
65 kDa phosphoprotein Chain: C
Molecule details ›
Chain: C
Length: 17 amino acids
Theoretical weight: 1.85 KDa
Source organism: Human herpesvirus 5 strain AD169
Expression system: Not provided
UniProt:
  • Canonical: P06725 (Residues: 142-158; Coverage: 3%)
Gene name: UL83

Ligands and Environments

3 bound ligands:
Ligand NAG 3 x NAG
Ligand GLY 1 x GLY
Ligand EDO 1 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: AUSTRALIAN SYNCHROTRON BEAMLINE MX2
Spacegroup: C2
Unit cell:
a: 112.36Å b: 62.364Å c: 72.796Å
α: 90° β: 91.523° γ: 90°
R-values:
R R work R free
0.183 0.181 0.224
Expression systems:
  • Insect expression vector pBlueBacmsGCA1His
  • Insect expression vector pBlueBacmsGCB1His
  • Not provided

Quick links

Citations

2 citation in other articles

Accurate prediction of HLA class II antigen presentation across all loci using tailored data acquisition and refined machine learning.
Nilsson et al. (2023)
1 more

1 mention without citation

Human T cells recognize HLA-DP-bound peptides in two orientations.
Klobuch et al. (2022)