› 6jq2

X-ray diffraction
2.4Å resolution

Crystal Structure of H2-Kb in complex with a DPAGT1 self-peptide

Released:
DOI: 10.2210/pdb6jq2/pdb
PDB entry 6jq2 coloured by chain, front view.
PDB entry 6jq2 coloured by chain, side view.
PDB entry 6jq2 coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
Immune-based mutation classification enables neoantigen prioritization and immune feature discovery in cancer immunotherapy.
Bai P, Li Y, Zhou Q, Xia J, Wei PC, Deng H, Wu M, Chan SK, Kappler JW, Zhou Y, Tran E, Marrack P, Yin L
Oncoimmunology 10 1868130 (2021)
PMID: 33537173

Function and Biology Details

Reaction catalysed: 
UDP-N-acetyl-D-glucosamine + dolichyl phosphate = UMP + N-acetyl-D-glucosaminyl-diphosphodolichol
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-135051 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
H-2 class I histocompatibility antigen, K-B alpha chain Chain: A
Molecule details ›
Chain: A
Length: 274 amino acids
Theoretical weight: 31.65 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: P01901 (Residues: 22-295; Coverage: 79%)
Gene names: H2-K, H2-K1
Sequence domains:
UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase Chain: P
Molecule details ›
Chain: P
Length: 8 amino acids
Theoretical weight: 904 Da
Source organism: Mus musculus
Expression system: Not provided
UniProt:
  • Canonical: P42867 (Residues: 206-213; Coverage: 2%)
Gene names: Dpagt1, Dpagt2, Gnpta
Beta-2-microglobulin Chain: B
Molecule details ›
Chain: B
Length: 99 amino acids
Theoretical weight: 11.66 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

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U1
Spacegroup: C2
Unit cell:
a: 107.24Å b: 69.42Å c: 70.44Å
α: 90° β: 103.79° γ: 90°
R-values:
R R work R free
0.226 0.221 0.275
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

3 review citations

Beyond Tumor Mutation Burden: Tumor Neoantigen Burden as a Biomarker for Immunotherapy and Other Types of Therapy.
Wang et al. (2021)
2 more