› 6gb5

X-ray diffraction
2.3Å resolution

Structure of H-2Db with truncated SEV peptide and GL

Released:
DOI: 10.2210/pdb6gb5/pdb
PDB entry 6gb5 coloured by chain, front view.
PDB entry 6gb5 coloured by chain, side view.
PDB entry 6gb5 coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
Successive crystal structure snapshots suggest the basis for MHC class I peptide loading and editing by tapasin.
Hafstrand I, Sayitoglu EC, Apavaloaei A, Josey BJ, Sun R, Han X, Pellegrino S, Ozkazanc D, Potens R, Janssen L, Nilvebrant J, Nygren PÅ, Sandalova T, Springer S, Georgoudaki AM, Duru AD, Achour A
Proc Natl Acad Sci U S A 116 5055-5060 (2019)
PMID: 30808808

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
PDBe Complex ID:
PDB-CPX-129583 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
H-2 class I histocompatibility antigen, D-B alpha chain Chains: A, C
Molecule details ›
Chains: A, C
Length: 338 amino acids
Theoretical weight: 38.45 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P01899 (Residues: 25-362; Coverage: 100%)
Gene name: H2-D1
Sequence domains:
Structure domains:
Beta-2-microglobulin Chains: B, D
Molecule details ›
Chains: B, D
Length: 99 amino acids
Theoretical weight: 11.7 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P01887 (Residues: 21-119; Coverage: 100%)
Gene name: B2m
Sequence domains: Immunoglobulin C1-set domain
Structure domains: Immunoglobulins
Nucleoprotein Chains: E, F
Molecule details ›
Chains: E, F
Length: 7 amino acids
Theoretical weight: 765 Da
UniProt:
  • Canonical: O57286 (Residues: 324-330; Coverage: 1%)
Gene names: N, NP
GLY-LEU Chains: G, H
Molecule details ›
Chains: G, H
Length: 2 amino acids
Theoretical weight: 188 Da
Source organism: Mus musculus
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand SO4 6 x SO4
Ligand GOL 3 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.1
Unit cell:
a: 91.93Å b: 123.36Å c: 99.206Å
α: 90° β: 103.73° γ: 90°
R-values:
R R work R free
0.2 0.198 0.24
Expression systems:
  • Escherichia coli BL21
  • Not provided

Quick links

Citations

5 review citations

Cancer Immune Evasion Through Loss of MHC Class I Antigen Presentation.
Dhatchinamoorthy et al. (2021)
4 more

1 mention without citation

Successive crystal structure snapshots suggest the basis for MHC class I peptide loading and editing by tapasin.
Hafstrand et al. (2019)