› 1n5a

X-ray diffraction
2.85Å resolution

Crystal structure of the Murine class I Major Histocompatibility Complex of H-2DB, B2-Microglobulin, and A 9-Residue immunodominant peptide epitope gp33 derived from LCMV

Released:
DOI: 10.2210/pdb1n5a/pdb
PDB entry 1n5a coloured by chain, front view.
PDB entry 1n5a coloured by chain, side view.
PDB entry 1n5a coloured by chain, top view.
Source organisms:
Primary publication:
A structural basis for LCMV immune evasion: subversion of H-2D(b) and H-2K(b) presentation of gp33 revealed by comparative crystal structure.Analyses.
Achour A, Michaëlsson J, Harris RA, Odeberg J, Grufman P, Sandberg JK, Levitsky V, Kärre K, Sandalova T, Schneider G
Immunity 17 757-68 (2002)
PMID: 12479822

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-135025 (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
Stable signal peptide Chains: C, F, I, L
Molecule details ›
Chains: C, F, I, L
Length: 9 amino acids
Theoretical weight: 1.05 KDa
Source organism: Mammarenavirus choriomeningitidis
Expression system: Not provided
UniProt:
  • Canonical: Q9QDK7 (Residues: 33-41; Coverage: 2%)
Gene name: 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: 91.998Å b: 122.657Å c: 99.18Å
α: 90° β: 103.34° γ: 90°
R-values:
R R work R free
0.253 0.251 0.279
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

2 review citations

Molecular pathways for antigenic peptide generation by ER aminopeptidase 1.
Mpakali et al. (2019)
1 more

3 mentions without citation

Modeling the structure of bound peptide ligands to major histocompatibility complex.
Tong et al. (2004)
2 more