› 7vpp

X-ray diffraction
2.69Å resolution

Structures of a deltacoronavirus spike protein bound to porcine and human receptors indicate the risk of virus adaptation to humans

Released:
DOI: 10.2210/pdb7vpp/pdb
PDB entry 7vpp coloured by chain, front view.
PDB entry 7vpp coloured by chain, side view.
PDB entry 7vpp coloured by chain, top view.
Source organisms:
Primary publication:
Structures of a deltacoronavirus spike protein bound to porcine and human receptors.
Ji W, Peng Q, Fang X, Li Z, Li Y, Xu C, Zhao S, Li J, Chen R, Mo G, Wei Z, Xu Y, Li B, Zhang S
Nat Commun 13 1467 (2022)
PMID: 35304871

Function and Biology Details

Reaction catalysed: 
Release of an N-terminal amino acid, Xaa-|-Yaa- from a peptide, amide or arylamide. Xaa is preferably Ala, but may be most amino acids including Pro (slow action). When a terminal hydrophobic residue is followed by a prolyl residue, the two may be released as an intact Xaa-Pro dipeptide.
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-105164 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (4 distinct):
Aminopeptidase N Chains: A, C
Molecule details ›
Chains: A, C
Length: 911 amino acids
Theoretical weight: 103.8 KDa
Source organism: Sus scrofa
Expression system: Baculovirus expression vector pFastBac1-HM
UniProt:
  • Canonical: P15145 (Residues: 58-961; Coverage: 94%)
Gene name: ANPEP
Sequence domains:
Spike protein Chain: B
Molecule details ›
Chain: B
Length: 127 amino acids
Theoretical weight: 14.33 KDa
Source organism: Porcine deltacoronavirus
Expression system: Baculovirus expression vector pFastBac1-HM
UniProt:
  • Canonical: A0A4P8D758 (Residues: 299-418; Coverage: 10%)
Sequence domains: Coronavirus spike glycoprotein S1

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
3 bound ligands:
Ligand ZN 2 x ZN
Ligand GOL 5 x GOL
Ligand NAG 5 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL02U1
Spacegroup: P41212
Unit cell:
a: 186.643Å b: 186.643Å c: 173.823Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.2 0.198 0.23
Expression system: Baculovirus expression vector pFastBac1-HM

Quick links

Citations

1 review citation

Reverse Genetics Systems for Emerging and Re-Emerging Swine Coronaviruses and Applications.
Jiang et al. (2023)
8 other articles