› 8d5j

X-ray diffraction
1.95Å resolution

The complex of Pre-mRNA-Processing Factor 19 (Prpf19) neoantigen KYLQVASHV Presented by H2-Kd

Released:
DOI: 10.2210/pdb8d5j/pdb
PDB entry 8d5j coloured by chain, front view.
PDB entry 8d5j coloured by chain, side view.
PDB entry 8d5j coloured by chain, top view.
Source organism: Mus musculus
Entry authors: Custodio JMF, Baker BM

Function and Biology Details

Reaction catalysed: 
S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-135068 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
H-2 class I histocompatibility antigen, K-D alpha chain Chain: A
Molecule details ›
Chain: A
Length: 276 amino acids
Theoretical weight: 32.25 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P01902 (Residues: 22-295; Coverage: 79%)
Gene names: H2-K, H2-K1
Sequence domains:
Beta-2-microglobulin Chain: B
Molecule details ›
Chain: B
Length: 100 amino acids
Theoretical weight: 11.84 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P01887 (Residues: 21-119; Coverage: 100%)
Gene name: B2m
Sequence domains: Immunoglobulin C1-set domain
Pre-mRNA-processing factor 19 Chain: C
Molecule details ›
Chain: C
Length: 9 amino acids
Theoretical weight: 1.05 KDa
Source organism: Mus musculus
Expression system: Not provided
UniProt:
  • Canonical: Q99KP6 (Residues: 206-214; Coverage: 2%)
Gene names: Prp19, Prpf19, Snev

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-E
Spacegroup: C2
Unit cell:
a: 115.44Å b: 66.57Å c: 56.96Å
α: 90° β: 92.01° γ: 90°
R-values:
R R work R free
0.188 0.186 0.23
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

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