› 5jil

X-ray diffraction
1.85Å resolution

Crystal structure of rat coronavirus strain New-Jersey Hemagglutinin-Esterase in complex with 4N-acetyl sialic acid

Released:
DOI: 10.2210/pdb5jil/pdb
PDB 5jil coloured by chain and viewed from the front.
PDB 5jil coloured by chain and viewed from the side.
PDB 5jil coloured by chain and viewed from the top.
Source organism: Rat coronavirus
Primary publication:
Coronavirus receptor switch explained from the stereochemistry of protein-carbohydrate interactions and a single mutation.
Bakkers MJ, Zeng Q, Feitsma LJ, Hulswit RJ, Li Z, Westerbeke A, van Kuppeveld FJ, Boons GJ, Langereis MA, Huizinga EG, de Groot RJ
Proc. Natl. Acad. Sci. U.S.A. (2016)
PMID: 27185912

Function and Biology Details

Reaction catalysed: 
N-acetyl-O-acetylneuraminate + H(2)O = N-acetylneuraminate + acetate
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (2 distinct):
Hemagglutinin-esterase Chain: A
Molecule details ›
Chain: A
Length: 388 amino acids
Theoretical weight: 43.61 KDa
Source organism: Rat coronavirus
Expression system: Homo sapiens
UniProt:
  • Canonical: Q3HS77 (Residues: 22-400; Coverage: 87%)
Gene name: HE
Sequence domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
4 bound ligands:
Ligand NAG 7 x NAG
Ligand NA 1 x NA
Ligand ZN 1 x ZN
Ligand 6KL 2 x 6KL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-2
Spacegroup: C2221
Unit cell:
a: 57.09Å b: 184.59Å c: 78.08Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.185 0.184 0.2
Expression system: Homo sapiens

Quick links

Citations

9 review citations

A Deadly Embrace: Hemagglutination Mediated by SARS-CoV-2 Spike Protein at Its 22 N-Glycosylation Sites, Red Blood Cell Surface Sialoglycoproteins, and Antibody.
Scheim DE. (2022)
8 more

2 mentions without citation

Coronavirus receptor switch explained from the stereochemistry of protein-carbohydrate interactions and a single mutation.
Bakkers et al. (2016)
1 more