› 6kwn

X-ray diffraction
2.4Å resolution

Crystal structure of pSLA-1*1301(F99Y) complex with S-OIV-derived epitope NSDTVGWSW

Released:
DOI: 10.2210/pdb6kwn/pdb
PDB entry 6kwn coloured by chain, front view.
PDB entry 6kwn coloured by chain, side view.
PDB entry 6kwn coloured by chain, top view.
Source organisms:
Primary publication:
Peptidomes and Structures Illustrate Two Distinguishing Mechanisms of Alternating the Peptide Plasticity Caused by Swine MHC Class I Micropolymorphism.
Wei X, Wang S, Li Z, Li Z, Qu Z, Wang S, Zou B, Liang R, Xia C, Zhang N
Front Immunol 12 592447 (2021)
PMID: 33717070

Function and Biology Details

Reaction catalysed: 
Hydrolysis of alpha-(2->3)-, alpha-(2->6)-, alpha-(2->8)- glycosidic linkages of terminal sialic acid residues in oligosaccharides, glycoproteins, glycolipids, colominic acid and synthetic substrates.
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-109390 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Ig-like domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 275 amino acids
Theoretical weight: 31.62 KDa
Source organism: Sus scrofa
Expression system: Escherichia coli
UniProt:
  • Canonical: B1PJU7 (Residues: 22-296; Coverage: 81%)
Gene name: SLA-1
Sequence domains:
Beta-2-microglobulin Chain: B
Molecule details ›
Chain: B
Length: 99 amino acids
Theoretical weight: 11.58 KDa
Source organism: Sus scrofa
Expression system: Escherichia coli
UniProt:
  • Canonical: Q07717 (Residues: 21-118; Coverage: 100%)
Gene name: B2M
Sequence domains: Immunoglobulin C1-set domain
Neuraminidase Chain: C
Molecule details ›
Chain: C
Length: 9 amino acids
Theoretical weight: 1.05 KDa
Source organism: Swine influenza virus
Expression system: Not provided
UniProt:
  • Canonical: Q9Q0U7 (Residues: 449-457; Coverage: 2%)
Gene name: NA

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL19U1
Spacegroup: C2
Unit cell:
a: 218.314Å b: 46.306Å c: 45.024Å
α: 90° β: 90.656° γ: 90°
R-values:
R R work R free
0.246 0.244 0.282
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

1 review citation

New vistas unfold: Chicken MHC molecules reveal unexpected ways to present peptides to the immune system.
Halabi et al. (2022)

2 mentions without citation

Peptidomes and Structures Illustrate Two Distinguishing Mechanisms of Alternating the Peptide Plasticity Caused by Swine MHC Class I Micropolymorphism.
Wei et al. (2021)
1 more