[English] 日本語
Yorodumi- PDB-9h0b: Crystal structure of the Porcine Hemagglutinating Encephalomyelit... -
+
Open data
-
Basic information
| Entry | Database: PDB / ID: 9h0b | ||||||
|---|---|---|---|---|---|---|---|
| Title | Crystal structure of the Porcine Hemagglutinating Encephalomyelitis Virus (PHEV) receptor binding domain in complex with porcine DPEP1. | ||||||
Components |
| ||||||
Keywords | VIRAL PROTEIN / RBD Receptor Spike Entry | ||||||
| Function / homology | Function and homology informationAflatoxin activation and detoxification / Synthesis of Leukotrienes (LT) and Eoxins (EX) / leukotriene D4 catabolic process / membrane dipeptidase / antibiotic metabolic process / GPI anchor binding / glutathione catabolic process / modified amino acid binding / homocysteine metabolic process / leukotriene metabolic process ...Aflatoxin activation and detoxification / Synthesis of Leukotrienes (LT) and Eoxins (EX) / leukotriene D4 catabolic process / membrane dipeptidase / antibiotic metabolic process / GPI anchor binding / glutathione catabolic process / modified amino acid binding / homocysteine metabolic process / leukotriene metabolic process / dipeptidase activity / metallodipeptidase activity / microvillus membrane / side of membrane / cellular response to nitric oxide / cellular response to calcium ion / negative regulation of cell migration / beta-lactamase activity / beta-lactamase / cellular response to insulin stimulus / apical part of cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / apical plasma membrane / endocytosis involved in viral entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / endoplasmic reticulum membrane / host cell plasma membrane / virion membrane / proteolysis / extracellular space / zinc ion binding / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
| Biological species | ![]() Porcine hemagglutinating encephalomyelitis virus | ||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Fernandez, I. / Rey, F. | ||||||
| Funding support | 1items
| ||||||
Citation | Journal: Nat Microbiol / Year: 2025Title: Dipeptidase 1 is a functional receptor for a porcine coronavirus. Authors: Jérémy Dufloo / Ignacio Fernández / Atousa Arbabian / Ahmed Haouz / Nigel Temperton / Luis G Gimenez-Lirola / Félix A Rey / Rafael Sanjuán / ![]() 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. | ||||||
| History |
|
-
Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
|---|
-
Downloads & links
-
Download
| PDBx/mmCIF format | 9h0b.cif.gz | 624.6 KB | Display | PDBx/mmCIF format |
|---|---|---|---|---|
| PDB format | pdb9h0b.ent.gz | 427 KB | Display | PDB format |
| PDBx/mmJSON format | 9h0b.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 9h0b_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
|---|---|---|---|---|
| Full document | 9h0b_full_validation.pdf.gz | 1.9 MB | Display | |
| Data in XML | 9h0b_validation.xml.gz | 57.6 KB | Display | |
| Data in CIF | 9h0b_validation.cif.gz | 78.3 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h0/9h0b ftp://data.pdbj.org/pub/pdb/validation_reports/h0/9h0b | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9h3jC ![]() 9r6oC ![]() 9r6pC ![]() 9r6qC ![]() 9r6rC C: citing same article ( |
|---|---|
| Similar structure data | Similarity search - Function & homology F&H Search |
-
Links
-
Assembly
| Deposited unit | ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Unit cell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
|
Movie
Controller
Components
About Yorodumi




Porcine hemagglutinating encephalomyelitis virus
X-RAY DIFFRACTION
Citation

















PDBj

