› 4is6

X-ray diffraction
2.5Å resolution

Crystal structure of HLA-DR4 bound to GP100 peptide

Released:
DOI: 10.2210/pdb4is6/pdb
PDB entry 4is6 coloured by chain, front view.
PDB entry 4is6 coloured by chain, side view.
PDB entry 4is6 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure-based design of altered MHC class II-restricted peptide ligands with heterogeneous immunogenicity.
Chen S, Li Y, Depontieu FR, McMiller TL, English AM, Shabanowitz J, Kos F, Sidney J, Sette A, Rosenberg SA, Hunt DF, Mariuzza RA, Topalian SL
J Immunol 191 5097-106 (2013)
PMID: 24108701

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-135337 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
HLA class II histocompatibility antigen, DR alpha chain Chain: A
Molecule details ›
Chain: A
Length: 182 amino acids
Theoretical weight: 21.16 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P01903 (Residues: 26-207; Coverage: 80%)
Gene names: HLA-DRA, HLA-DRA1
Sequence domains:
Structure domains:
HLA class II histocompatibility antigen, DRB1 beta chain Chain: B
Molecule details ›
Chain: B
Length: 192 amino acids
Theoretical weight: 22.52 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P01911 (Residues: 30-221; Coverage: 81%)
Gene name: HLA-DRB1
Sequence domains:
Structure domains:
M-alpha Chain: C
Molecule details ›
Chain: C
Length: 16 amino acids
Theoretical weight: 2.11 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P40967 (Residues: 44-59; Coverage: 3%)
Gene names: D12S53E, PMEL, PMEL17, SILV

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X29A
Spacegroup: P21212
Unit cell:
a: 90.29Å b: 117.59Å c: 41.89Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.265 0.265 0.298
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

4 review citations

On Peptides and Altered Peptide Ligands: From Origin, Mode of Action and Design to Clinical Application (Immunotherapy).
Candia et al. (2016)
3 more

11 mentions without citation

Accurate pan-specific prediction of peptide-MHC class II binding affinity with improved binding core identification.
Andreatta et al. (2015)
10 more