› 7s79

X-ray diffraction
1.53Å resolution

STRUCTURE OF HLA-B*07:02 IN COMPLEX WITH SYNTHETIC PHOSPHONO-MLL PEPTIDE ANALOG

Released:
DOI: 10.2210/pdb7s79/pdb
PDB entry 7s79 coloured by chain, front view.
PDB entry 7s79 coloured by chain, side view.
PDB entry 7s79 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: 
S-adenosyl-L-methionine + a [histone H3]-L-lysine(4) = S-adenosyl-L-homocysteine + a [histone H3]-N(6)-methyl-L-lysine(4)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-135242 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 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
MLL cleavage product N320 Chain: E
Molecule details ›
Chain: E
Length: 9 amino acids
Theoretical weight: 1.11 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: Q03164 (Residues: 747-755; Coverage: 0%)
Gene names: ALL1, CXXC7, HRX, HTRX, KMT2A, MLL, MLL1, TRX1

Ligands and Environments

2 bound ligands:
Ligand GOL 4 x GOL
Ligand NA 1 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS-II BEAMLINE 17-ID-2
Spacegroup: P41212
Unit cell:
a: 65.86Å b: 65.86Å c: 238.857Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.171 0.17 0.196
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)