› 5ib3

X-ray diffraction
1.91Å resolution

Crystal structure of HLA-B*27:05 complexed with the self-peptide pVIPR and Copper

Released:
DOI: 10.2210/pdb5ib3/pdb
PDB entry 5ib3 coloured by chain, front view.
PDB entry 5ib3 coloured by chain, side view.
PDB entry 5ib3 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Metal-triggered conformational reorientation of a self-peptide bound to a disease-associated HLA-B*27 subtype.
Driller R, Ballaschk M, Schmieder P, Uchanska-Ziegler B, Ziegler A, Loll B
J Biol Chem 294 13269-13279 (2019)
PMID: 31296658

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-135160 (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: 31.93 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
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: 100 amino acids
Theoretical weight: 11.88 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P61769 (Residues: 21-119; Coverage: 100%)
Gene names: B2M, CDABP0092, HDCMA22P
Sequence domains: Immunoglobulin C1-set domain
Structure domains: Immunoglobulins
Vasoactive intestinal polypeptide receptor 1 Chain: C
Molecule details ›
Chain: C
Length: 9 amino acids
Theoretical weight: 1.4 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P32241 (Residues: 400-408; Coverage: 2%)
Gene name: VIPR1

Ligands and Environments

2 bound ligands:
Ligand CU 2 x CU
Ligand GOL 2 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)
Spacegroup: P21
Unit cell:
a: 51.295Å b: 82.129Å c: 65.362Å
α: 90° β: 107.56° γ: 90°
R-values:
R R work R free
0.171 0.17 0.204
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

1 review citation

The Impact of the 'Mis-Peptidome' on HLA Class I-Mediated Diseases: Contribution of ERAP1 and ERAP2 and Effects on the Immune Response.
Tedeschi et al. (2020)
3 other articles

1 mention without citation

Metal-triggered conformational reorientation of a self-peptide bound to a disease-associated HLA-B*27 subtype.
Driller et al. (2019)