› 7s7f

X-ray diffraction
1.88Å resolution

STRUCTURE OF HLA-B*07:02 IN COMPLEX WITH DOT1L(998-1006) PHOSPHOPEPTIDE

Released:
DOI: 10.2210/pdb7s7f/pdb
PDB entry 7s7f coloured by chain, front view.
PDB entry 7s7f coloured by chain, side view.
PDB entry 7s7f coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Molecular mechanism of phosphopeptide neoantigen immunogenicity.
Patskovsky Y, Natarajan A, Patskovska L, Nyovanie S, Joshi B, Morin B, Brittsan C, Huber O, Gordon S, Michelet X, Schmitzberger F, Stein RB, Findeis MA, Hurwitz A, Van Dijk M, Chantzoura E, Yague AS, Pollack Smith D, Buell JS, Underwood D, Krogsgaard M
Nat Commun 14 3763 (2023)
PMID: 37353482

Function and Biology Details

Reaction catalysed: 
(1a) S-adenosyl-L-methionine + a [histone H3]-L-lysine(79) = S-adenosyl-L-homocysteine + a [histone H3]-N(6)-methyl-L-lysine(79)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-135255 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (4 distinct):
HLA class I histocompatibility antigen, B alpha chain Chain: A
Molecule details ›
Chain: A
Length: 275 amino acids
Theoretical weight: 31.96 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P01889 (Residues: 25-299; Coverage: 81%)
Gene names: HLA-B, HLAB
Sequence domains:
Beta-2-microglobulin Chain: B
Molecule details ›
Chain: B
Length: 100 amino acids
Theoretical weight: 11.88 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P61769 (Residues: 21-119; Coverage: 100%)
Gene names: B2M, CDABP0092, HDCMA22P
Sequence domains: Immunoglobulin C1-set domain
Histone-lysine N-methyltransferase, H3 lysine-79 specific Chain: C
Molecule details ›
Chain: C
Length: 9 amino acids
Theoretical weight: 1.01 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: Q8TEK3 (Residues: 998-1006; Coverage: 1%)
Gene names: DOT1L, KIAA1814, KMT4

Ligands and Environments

Carbohydrate polymer : NEW Components: GLC, FRU
Carbohydrate polymer
No bound ligands
1 modified residue:
Ligand SEP 1 x SEP

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS-II BEAMLINE 17-ID-2
Spacegroup: P41212
Unit cell:
a: 65.767Å b: 65.767Å c: 239.078Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.17 0.168 0.217
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

1 citations in other articles

The landscape of MHC-presented phosphopeptides yields actionable shared tumor antigens for cancer immunotherapy across multiple HLA alleles.
Molvi et al. (2023)