› 6jtp

X-ray diffraction
1.9Å resolution

Crystal structure of HLA-C08 in complex with a tumor mut9m peptide

Released:
DOI: 10.2210/pdb6jtp/pdb
PDB entry 6jtp coloured by chain, front view.
PDB entry 6jtp coloured by chain, side view.
PDB entry 6jtp coloured by chain, top view.
Source organism: Homo sapiens
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: 
GTP + H(2)O = GDP + phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-111136 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Ig-like domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 273 amino acids
Theoretical weight: 31.73 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: C1K0Y1 (Residues: 26-298; Coverage: 80%)
Gene names: HLA-C, HLA-Cw
Sequence domains:
Beta-2-microglobulin Chain: B
Molecule details ›
Chain: B
Length: 98 amino acids
Theoretical weight: 11.62 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: P61769 (Residues: 21-118; Coverage: 99%)
Gene names: B2M, CDABP0092, HDCMA22P
Sequence domains: Immunoglobulin C1-set domain
GTPase KRas, N-terminally processed Chain: C
Molecule details ›
Chain: C
Length: 9 amino acids
Theoretical weight: 762 Da
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P01116 (Residues: 10-18; Coverage: 5%)
Gene names: KRAS, KRAS2, RASK2

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U1
Spacegroup: P212121
Unit cell:
a: 68.28Å b: 75.92Å c: 78.03Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.242 0.24 0.283
Expression systems:
  • Escherichia coli K-12
  • 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

1 mention without citation

Immune-based mutation classification enables neoantigen prioritization and immune feature discovery in cancer immunotherapy.
Bai et al. (2021)