› 3qul

X-ray diffraction
2Å resolution

Crystal structures of the murine class I major histocompatibility complex H-2Db in complex with LCMV-derived gp33 altered peptide ligand (Y4S)

Released:
DOI: 10.2210/pdb3qul/pdb
PDB entry 3qul coloured by chain, front view.
PDB entry 3qul coloured by chain, side view.
PDB entry 3qul coloured by chain, top view.
Source organisms:
Primary publication:
Unexpected T-cell recognition of an altered peptide ligand is driven by reversed thermodynamics.
Allerbring EB, Duru AD, Uchtenhagen H, Madhurantakam C, Tomek MB, Grimm S, Mazumdar PA, Friemann R, Uhlin M, Sandalova T, Nygren PÅ, Achour A
Eur J Immunol 42 2990-3000 (2012)
PMID: 22837158

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-134985 (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 BL21(DE3)
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 BL21(DE3)
UniProt:
  • Canonical: P01887 (Residues: 21-119; Coverage: 100%)
Gene name: B2m
Sequence domains: Immunoglobulin C1-set domain
Structure domains: Immunoglobulins
Stable signal peptide Chains: C, F, I, L
Molecule details ›
Chains: C, F, I, L
Length: 9 amino acids
Theoretical weight: 969 Da
Source organism: Lymphocytic choriomeningitis virus (strain WE)
Expression system: Not provided
UniProt:
  • Canonical: P07399 (Residues: 33-41; Coverage: 2%)
Gene names: GP-C, GPC

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: MAX II BEAMLINE I711
Spacegroup: P21
Unit cell:
a: 92.041Å b: 122.697Å c: 99.123Å
α: 90° β: 103.33° γ: 90°
R-values:
R R work R free
0.209 0.208 0.234
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

8 citation in other articles

Structural basis for ineffective T-cell responses to MHC anchor residue-improved "heteroclitic" peptides.
Madura et al. (2015)
7 more