› 1xr9

X-ray diffraction
1.79Å resolution

Crystal Structures of HLA-B*1501 in Complex with Peptides from Human UbcH6 and Epstein-Barr Virus EBNA-3

Released:
DOI: 10.2210/pdb1xr9/pdb
PDB entry 1xr9 coloured by chain, front view.
PDB entry 1xr9 coloured by chain, side view.
PDB entry 1xr9 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Crystal structures of two peptide-HLA-B*1501 complexes; structural characterization of the HLA-B62 supertype.
Røder G, Blicher T, Justesen S, Johannesen B, Kristensen O, Kastrup J, Buus S, Gajhede M
Acta Crystallogr D Biol Crystallogr 62 1300-10 (2006)
PMID: 17057332

Function and Biology Details

Reactions catalysed: 
S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine + [E2 ubiquitin-conjugating enzyme]-L-cysteine = [E1 ubiquitin-activating enzyme]-L-cysteine + S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine
(1a) S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine + [(E3-independent) E2 ubiquitin-conjugating enzyme]-L-cysteine = [E1 ubiquitin-activating enzyme]-L-cysteine + S-monoubiquitinyl-[(E3-independent) ubiquitin-conjugating enzyme]-L-cysteine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-135167 (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: 276 amino acids
Theoretical weight: 31.96 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P01889 (Residues: 25-300; Coverage: 82%)
Gene names: HLA-B, HLAB
Sequence domains:
Structure domains:
Beta-2-microglobulin Chain: B
Molecule details ›
Chain: B
Length: 99 amino acids
Theoretical weight: 11.75 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
Structure domains: Immunoglobulins
Ubiquitin-conjugating enzyme E2 E1 Chain: C
Molecule details ›
Chain: C
Length: 9 amino acids
Theoretical weight: 902 Da
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P51965 (Residues: 83-91; Coverage: 5%)
Gene names: UBCH6, UBE2E1

Ligands and Environments

3 bound ligands:
Ligand SO4 2 x SO4
Ligand URE 1 x URE
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: EMBL/DESY, HAMBURG BEAMLINE BW7B
Spacegroup: P212121
Unit cell:
a: 50.359Å b: 81.389Å c: 109.969Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.18 0.177 0.232
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

1 review citation

HLA-associated antiepileptic drug-induced cutaneous adverse reactions.
Mullan et al. (2019)
10 other articles

16 mentions without citation

Mechano-regulation of Peptide-MHC Class I Conformations Determines TCR Antigen Recognition.
Wu et al. (2019)
15 more