› 3ch1

X-ray diffraction
2.3Å resolution

Crystal structure of H-2Db in complex with chimeric gp100

Released:
DOI: 10.2210/pdb3ch1/pdb
PDB entry 3ch1 coloured by chain, front view.
PDB entry 3ch1 coloured by chain, side view.
PDB entry 3ch1 coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
Design of agonistic altered peptides for the robust induction of CTL directed towards H-2Db in complex with the melanoma-associated epitope gp100.
van Stipdonk MJ, Badia-Martinez D, Sluijter M, Offringa R, van Hall T, Achour A
Cancer Res 69 7784-92 (2009)
PMID: 19789338

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-135002 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
H-2 class I histocompatibility antigen, D-B alpha chain Chains: A, D, G, J
Molecule details ›
Chains: A, D, G, J
Length: 276 amino acids
Theoretical weight: 32.09 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: P01899 (Residues: 25-300; Coverage: 82%)
Gene name: H2-D1
Sequence domains:
Structure domains:
Beta-2-microglobulin Chains: B, E, H, K
Molecule details ›
Chains: B, E, H, K
Length: 99 amino acids
Theoretical weight: 11.7 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: P01887 (Residues: 21-119; Coverage: 100%)
Gene name: B2m
Sequence domains: Immunoglobulin C1-set domain
Structure domains: Immunoglobulins
nonameric peptide chimeric gp100 Chains: C, F, I, L
Molecule details ›
Chains: C, F, I, L
Length: 9 amino acids
Theoretical weight: 1.12 KDa

Ligands and Environments

2 bound ligands:
Ligand GOL 26 x GOL
Ligand SO4 5 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-1
Spacegroup: P2
Unit cell:
a: 104.5Å b: 105.4Å c: 126.69Å
α: 90° β: 90.08° γ: 90°
R-values:
R R work R free
0.233 0.231 0.264
Expression system: Escherichia coli

Quick links

Citations

7 review citations

Biomaterials for nanoparticle vaccine delivery systems.
Sahdev et al. (2014)
6 more

1 mention without citation

Structural allele-specific patterns adopted by epitopes in the MHC-I cleft and reconstruction of MHC:peptide complexes to cross-reactivity assessment.
Antunes et al. (2010)