› 2zol

X-ray diffraction
2.7Å resolution

Crystal structure of H-2Db in complex with the W513S variant of JHMV epitope S510

Released:
DOI: 10.2210/pdb2zol/pdb
PDB entry 2zol coloured by chain, front view.
PDB entry 2zol coloured by chain, side view.
PDB entry 2zol coloured by chain, top view.
Source organisms:
Primary publication:
Structural and biological basis of CTL escape in coronavirus-infected mice.
Butler NS, Theodossis A, Webb AI, Dunstone MA, Nastovska R, Ramarathinam SH, Rossjohn J, Purcell AW, Perlman S
J Immunol 180 3926-37 (2008)
PMID: 18322201

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
hetero trimer (preferred)
hetero hexamer
PDBe Complex ID:
PDB-CPX-135015 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
H-2 class I histocompatibility antigen, D-B alpha chain Chains: A, C
Molecule details ›
Chains: A, C
Length: 278 amino acids
Theoretical weight: 32.46 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: P01899 (Residues: 25-299; Coverage: 81%)
Gene name: H2-D1
Sequence domains:
Structure domains:
Beta-2-microglobulin Chains: B, D
Molecule details ›
Chains: B, D
Length: 100 amino acids
Theoretical weight: 11.84 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
Spike protein S1 Chains: E, F
Molecule details ›
Chains: E, F
Length: 9 amino acids
Theoretical weight: 910 Da
Source organism: Murine hepatitis virus strain JHMV / variant CL-2
Expression system: Not provided
UniProt:
  • Canonical: Q02385 (Residues: 511-518; Coverage: 1%)
Gene names: 3, S

Ligands and Environments

1 bound ligand:
Ligand SO4 1 x SO4
1 modified residue:
Ligand ABA 2 x ABA

Experiments and Validation Details

Entry percentile scores
X-ray source: AUSTRALIAN SYNCHROTRON BEAMLINE MX1
Spacegroup: P2
Unit cell:
a: 83.561Å b: 71.033Å c: 86.999Å
α: 90° β: 103.45° γ: 90°
R-values:
R R work R free
0.256 0.254 0.307
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

1 review citation

Enhancing Human Immunodeficiency Virus-Specific CD8(+) T Cell Responses with Heteroclitic Peptides.
Adegoke et al. (2015)
12 other articles

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)