9R6Q | pdb_00009r6q

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

• PDB DOI: https://doi.org/10.2210/pdb9R6Q/pdb
• EM Map EMD-53684: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Porcine hemagglutinating encephalomyelitis virus
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2025-05-13 Released: 2025-08-06 
• Deposition Author(s): Fernandez, I., Rey, F.A.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Dipeptidase 1 is a functional receptor for a porcine coronavirus.

Dufloo, J., Fernandez, I., Arbabian, A., Haouz, A., Temperton, N., Gimenez-Lirola, L.G., Rey, F.A., Sanjuan, R.

(2025) Nat Microbiol 10: 2981-2996

• PubMed: 41073662 
• DOI: https://doi.org/10.1038/s41564-025-02111-7
• Primary Citation Related Structures: 
  9H0B, 9H3J, 9R6O, 9R6P, 9R6Q, 9R6R


• 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.

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Organizational Affiliation: 
• Institute for Integrative Systems Biology, CSIC-Universitat de València, Paterna, València, Spain.
Institut Pasteur, Université Paris Cité, CNRS UMR 3569, Structural Virology Unit, Paris, France.
Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Crystallography Facility-C2RT, Paris, France.
Viral Pseudotype Unit, Medway School of Pharmacy, Universities of Kent and Greenwich, Chatham, UK.
Department of Veterinary Diagnostic and Production Animal Medicine, Iowa State University, Ames, IA, USA.
Institut Pasteur, Université Paris Cité, CNRS UMR 3569, Structural Virology Unit, Paris, France. [e-mail].
Institute for Integrative Systems Biology, CSIC-Universitat de València, Paterna, València, Spain. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 297.15 kDa 
• Atom Count: 4,280 
• Modeled Residue Count: 535 
• Deposited Residue Count: 2,666 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, B	1,333	Porcine hemagglutinating encephalomyelitis virus	Mutation(s): 0
UniProt
Find proteins for Q2QKN3 (Porcine hemagglutinating encephalomyelitis virus) Explore Q2QKN3  Go to UniProtKB:  Q2QKN3
Glycosylation
Glycosylation Sites: 1

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C [auth D]	3		N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5N6 (Subject of Investigation/LOI)	E [auth A]	9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid C13 H21 N O10 NYWZBRWKDRMPAS-CTAKWSDESA-N
NAG	D [auth A], F [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-08-06 
Deposition Author(s): Fernandez, I., Rey, F.A.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-08-06
  Type: Initial release
  
• Version 1.1: 2025-10-22
  Changes: Data collection, Database references
• Version 1.2: 2025-11-12
  Changes: Data collection, Database references