9R6Q

Local refinement of the N-terminal domain (NTD) and receptor binding domain (RBD) from the Porcine hemagglutinating encephalomyelitis virus (PHEV) Spike in the closed conformation bound to 9-O-Ac-Sia

Summary for 9R6Q

• Entry DOI: 10.2210/pdb9r6q/pdb
• Related: 9H3J 9R6P 9R6Q 9R6R
• EMDB information: 51827 51844 51845 51846 53680 53681 53682 53683 53684 53684 53685
• Descriptor: Spike glycoprotein, beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose, ... (4 entities in total)
• Functional Keywords: coronavirus, spike, entry, viral protein
• Biological source: Porcine hemagglutinating encephalomyelitis virus
• Total number of polymer chains: 2
• Total formula weight: 297149.77

Authors

Fernandez, I.,Rey, F.A. (deposition date: 2025-05-13, release date: 2025-08-06, Last modification date: 2025-11-12)

Primary citation

Dufloo, J.,Fernandez, I.,Arbabian, A.,Haouz, A.,Temperton, N.,Gimenez-Lirola, L.G.,Rey, F.A.,Sanjuan, R.
Dipeptidase 1 is a functional receptor for a porcine coronavirus.
Nat Microbiol, 10:2981-2996, 2025

PubMed Abstract: Coronaviruses of the subgenus Embecovirus include several important pathogens, such as the human seasonal coronaviruses HKU1 and OC43, bovine coronavirus and porcine haemagglutinating encephalomyelitis virus (PHEV). While sialic acid is thought to be required for embecovirus entry, protein receptors remain unknown for most of these viruses. Here we show that PHEV does not require sialic acid for entry and instead uses dipeptidase 1 (DPEP1) as a receptor. Cryo-electron microscopy at 3.4-4.4 Å resolution revealed that, unlike other embecoviruses, PHEV displays both open and closed conformations of its spike trimer at steady state. The spike receptor-binding domain (RBD) exhibits extremely high sequence variability across embecoviruses, and we found that DPEP1 usage is specific to PHEV. In contrast, the X-ray structure of the RBD-DPEP1 complex at 2.25 Å showed that the structural elements involved in receptor binding are conserved, highlighting the remarkable versatility of this structural organization in adopting novel receptor specificities.

PubMed: 41073662
DOI: 10.1038/s41564-025-02111-7

Experimental method

ELECTRON MICROSCOPY (3.5 Å)