7US9 | pdb_00007us9

CCoV-HuPn-2018 S in the proximal conformation (local refinement of domain 0)

• PDB DOI: https://doi.org/10.2210/pdb7US9/pdb
• EM Map EMD-26729: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): unidentified human coronavirus
• Expression System: mammal environmental sample
• Mutation(s): No 


• Deposited: 2022-04-23 Released: 2022-08-24 
• Deposition Author(s): Tortorici, M.A., Veesler, D., Seattle Structural Genomics Center for Infectious Disease (SSGCID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure, receptor recognition, and antigenicity of the human coronavirus CCoV-HuPn-2018 spike glycoprotein.

Tortorici, M.A., Walls, A.C., Joshi, A., Park, Y.J., Eguia, R.T., Miranda, M.C., Kepl, E., Dosey, A., Stevens-Ayers, T., Boeckh, M.J., Telenti, A., Lanzavecchia, A., King, N.P., Corti, D., Bloom, J.D., Veesler, D.

(2022) Cell 185: 2279-2291.e17

• PubMed: 35700730 
• DOI: https://doi.org/10.1016/j.cell.2022.05.019
• Primary Citation Related Structures: 
  7U0L, 7US6, 7US9, 7USA, 7USB


• PubMed Abstract: 
  

  The isolation of CCoV-HuPn-2018 from a child respiratory swab indicates that more coronaviruses are spilling over to humans than previously appreciated. We determined the structures of the CCoV-HuPn-2018 spike glycoprotein trimer in two distinct conformational states and showed that its domain 0 recognizes sialosides. We identified that the CCoV-HuPn-2018 spike binds canine, feline, and porcine aminopeptidase N (APN) orthologs, which serve as entry receptors, and determined the structure of the receptor-binding B domain in complex with canine APN. The introduction of an oligosaccharide at position N739 of human APN renders cells susceptible to CCoV-HuPn-2018 spike-mediated entry, suggesting that single-nucleotide polymorphisms might account for viral detection in some individuals. Human polyclonal plasma antibodies elicited by HCoV-229E infection and a porcine coronavirus monoclonal antibody inhibit CCoV-HuPn-2018 spike-mediated entry, underscoring the cross-neutralizing activity among ɑ-coronaviruses. These data pave the way for vaccine and therapeutic development targeting this zoonotic pathogen representing the eighth human-infecting coronavirus.

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Organizational Affiliation: 
• Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA.
Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
Vir Biotechnology, San Francisco, CA 94158, USA.
Istituto Nazionale Genetica Molecolare, 20122 Milano, Italy; Humabs Biomed SA-a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland.
Humabs Biomed SA-a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland.
Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 30.83 kDa 
• Atom Count: 1,127 
• Modeled Residue Count: 145 
• Deposited Residue Count: 267 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A	267	unidentified human coronavirus	Mutation(s): 0
UniProt
Find proteins for A0A8E6CMP0 (Canine coronavirus) Explore A0A8E6CMP0  Go to UniProtKB:  A0A8E6CMP0
Glycosylation
Glycosylation Sites: 3

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C [auth A], D [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-08-24 
Deposition Author(s): Tortorici, M.A., Veesler, D., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History  

• Version 1.0: 2022-08-24
  Type: Initial release
  
• Version 1.1: 2024-10-30
  Changes: Data collection, Structure summary