Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Dipeptidase 1 is a functional receptor for a porcine coronavirus.
Journal, issue, pages	Nat Microbiol, Vol. 10, Issue 11, Page 2981-2996, Year 2025
Publish date	Oct 10, 2025
Authors	Jérémy Dufloo / Ignacio Fernández / Atousa Arbabian / Ahmed Haouz / Nigel Temperton / Luis G Gimenez-Lirola / Félix A Rey / Rafael Sanjuán /
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 ...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.
External links	Nat Microbiol / PubMed:41073662 / PubMed Central
Methods	EM (single particle) / X-ray diffraction
Resolution	2.25 - 4.1 Å
Structure data	51827 9h3j EMDB-51827, PDB-9h3j: Porcine hemagglutinating encephalomyelitis virus (PHEV) Spike in the closed conformation, apo state Method: EM (single particle) / Resolution: 3.5 Å EMDB-51844: Porcine hemagglutinating encephalomyelitis virus (PHEV) Spike in the 1-RBD-up conformation Method: EM (single particle) / Resolution: 3.6 Å EMDB-51845: Porcine hemagglutinating encephalomyelitis virus (PHEV) Spike protein in the 2-RBD-up conformation Method: EM (single particle) / Resolution: 3.7 Å EMDB-51846: Porcine hemagglutinating encephalomyelitis virus (PHEV) Spike protein in the open conformation Method: EM (single particle) / Resolution: 3.9 Å 53679 9r6o EMDB-53679, PDB-9r6o: 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 Method: EM (single particle) / Resolution: 4.1 Å 53680 9r6p EMDB-53680, PDB-9r6p: Porcine hemagglutinating encephalomyelitis virus (PHEV) Spike protein in the closed conformation bound to 9-O-Ac-Sia. Method: EM (single particle) / Resolution: 3.1 Å EMDB-53681: Porcine hemagglutinating encephalomyelitis virus (PHEV) Spike protein in the 1-RBD-up conformation, bound to 9-O-Ac-Sia Method: EM (single particle) / Resolution: 3.3 Å EMDB-53682: Porcine hemagglutinating encephalomyelitis virus (PHEV) Spike protein in the 2-RBD-up conformation, bound to 9-O-Ac-Sia Method: EM (single particle) / Resolution: 3.1 Å EMDB-53683: Porcine hemagglutinating encephalomyelitis virus (PHEV) Spike protein in the open conformation, bound to 9-O-Ac-Sia Method: EM (single particle) / Resolution: 3.0 Å 53684 9r6q EMDB-53684, PDB-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 Method: EM (single particle) / Resolution: 3.5 Å 53685 9r6r EMDB-53685, PDB-9r6r: Local refinement of the N-terminal domain (NTD) from the Porcine hemagglutinating encephalomyelitis virus (PHEV) Spike in the open conformation bound to 9-O-Ac-Sia Method: EM (single particle) / Resolution: 3.3 Å PDB-9h0b: Crystal structure of the Porcine Hemagglutinating Encephalomyelitis Virus (PHEV) receptor binding domain in complex with porcine DPEP1. Method: X-RAY DIFFRACTION / Resolution: 2.25 Å
Chemicals	ChemComp-ZN: Unknown entry ChemComp-NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose ChemComp-HOH: WATER ChemComp-5N6: 9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid
Source	porcine hemagglutinating encephalomyelitis virus Porcine hemagglutinating encephalomyelitis virus sus scrofa (pig)
Keywords	VIRAL PROTEIN / RBD Receptor Spike Entry / Coronavirus / Spike / Entry / glycoprotein