7USA | pdb_00007usa

Structure of the human coronavirus CCoV-HuPn-2018 spike glycoprotein with domain 0 in the swung out conformation

PDB DOI: https://doi.org/10.2210/pdb7USA/pdb
EM Map EMD-26730: 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)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.80 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

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 Search on PubMed Search on PubMed Central
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.

Organizational Affiliation

Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.

Macromolecule Content

Total Structure Weight: 503.93 kDa
Atom Count: 24,307
Modeled Residue Count: 3,181
Deposited Residue Count: 4,407
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, B, C	1,469	unidentified human coronavirus	Mutation(s): 0
UniProt
Find proteins for A0A8E6CMP0 (Canine coronavirus) Explore A0A8E6CMP0 Go to UniProtKB: A0A8E6CMP0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A8E6CMP0
Glycosylation
Glycosylation Sites: 19	Glycosylation Focus chain A Focus chain B Focus chain C
Sequence Annotations Expand
Reference Sequence

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	AA [auth a], CA [auth c], D, E, F, AA [auth a], CA [auth c], D, E, F, G, H, I, K, M, N, O, P, Q, R, T, V, W, X, Y, Z	2		N-Glycosylation	Interactions Focus chain AA [auth a] Focus chain CA [auth c] Focus chain D Focus chain E Focus chain F Focus chain G Focus chain H Focus chain I Focus chain K Focus chain M Focus chain N Focus chain O Focus chain P Focus chain Q Focus chain R Focus chain T Focus chain V Focus chain W Focus chain X Focus chain Y Focus chain Z Interactions & Density Focus chain AA [auth a] Focus chain CA [auth c] Focus chain D Focus chain E Focus chain F Focus chain G Focus chain H Focus chain I Focus chain K Focus chain M Focus chain N Focus chain O Focus chain P Focus chain Q Focus chain R Focus chain T Focus chain V Focus chain W Focus chain X Focus chain Y Focus chain Z
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 3
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	BA [auth b], DA [auth d], J, L, S, BA [auth b], DA [auth d], J, L, S, U	3		N-Glycosylation	Interactions Focus chain BA [auth b] Focus chain DA [auth d] Focus chain J Focus chain L Focus chain S Focus chain U Interactions & Density Focus chain BA [auth b] Focus chain DA [auth d] Focus chain J Focus chain L Focus chain S Focus chain U
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain ZA [auth C] SDF format, chain YA [auth C] SDF format, chain XA [auth B] SDF format, chain WA [auth B] SDF format, chain VA [auth B] SDF format, chain UA [auth B] SDF format, chain TA [auth B] SDF format, chain SA [auth B] SDF format, chain RA [auth B] SDF format, chain QA [auth B] SDF format, chain PA [auth B] SDF format, chain OA [auth B] SDF format, chain NA [auth A] SDF format, chain MA [auth A] SDF format, chain LA [auth A] SDF format, chain KA [auth A] SDF format, chain JA [auth A] SDF format, chain IA [auth A] SDF format, chain HB [auth C] SDF format, chain HA [auth A] SDF format, chain GB [auth C] SDF format, chain GA [auth A] SDF format, chain FB [auth C] SDF format, chain FA [auth A] SDF format, chain EB [auth C] SDF format, chain EA [auth A] SDF format, chain DB [auth C] SDF format, chain CB [auth C] SDF format, chain BB [auth C] SDF format, chain AB [auth C] MOL2 format, chain ZA [auth C] MOL2 format, chain YA [auth C] MOL2 format, chain XA [auth B] MOL2 format, chain WA [auth B] MOL2 format, chain VA [auth B] MOL2 format, chain UA [auth B] MOL2 format, chain TA [auth B] MOL2 format, chain SA [auth B] MOL2 format, chain RA [auth B] MOL2 format, chain QA [auth B] MOL2 format, chain PA [auth B] MOL2 format, chain OA [auth B] MOL2 format, chain NA [auth A] MOL2 format, chain MA [auth A] MOL2 format, chain LA [auth A] MOL2 format, chain KA [auth A] MOL2 format, chain JA [auth A] MOL2 format, chain IA [auth A] MOL2 format, chain HB [auth C] MOL2 format, chain HA [auth A] MOL2 format, chain GB [auth C] MOL2 format, chain GA [auth A] MOL2 format, chain FB [auth C] MOL2 format, chain FA [auth A] MOL2 format, chain EB [auth C] MOL2 format, chain EA [auth A] MOL2 format, chain DB [auth C] MOL2 format, chain CB [auth C] MOL2 format, chain BB [auth C] MOL2 format, chain AB [auth C] mmCIF format, chain ZA [auth C] mmCIF format, chain YA [auth C] mmCIF format, chain XA [auth B] mmCIF format, chain WA [auth B] mmCIF format, chain VA [auth B] mmCIF format, chain UA [auth B] mmCIF format, chain TA [auth B] mmCIF format, chain SA [auth B] mmCIF format, chain RA [auth B] mmCIF format, chain QA [auth B] mmCIF format, chain PA [auth B] mmCIF format, chain OA [auth B] mmCIF format, chain NA [auth A] mmCIF format, chain MA [auth A] mmCIF format, chain LA [auth A] mmCIF format, chain KA [auth A] mmCIF format, chain JA [auth A] mmCIF format, chain IA [auth A] mmCIF format, chain HB [auth C] mmCIF format, chain HA [auth A] mmCIF format, chain GB [auth C] mmCIF format, chain GA [auth A] mmCIF format, chain FB [auth C] mmCIF format, chain FA [auth A] mmCIF format, chain EB [auth C] mmCIF format, chain EA [auth A] mmCIF format, chain DB [auth C] mmCIF format, chain CB [auth C] mmCIF format, chain BB [auth C] mmCIF format, chain AB [auth C]	AB [auth C] BB [auth C] CB [auth C] DB [auth C] EA [auth A] AB [auth C], BB [auth C], CB [auth C], DB [auth C], EA [auth A], EB [auth C], FA [auth A], FB [auth C], GA [auth A], GB [auth C], HA [auth A], HB [auth C], IA [auth A], JA [auth A], KA [auth A], LA [auth A], MA [auth A], NA [auth A], OA [auth B], PA [auth B], QA [auth B], RA [auth B], SA [auth B], TA [auth B], UA [auth B], VA [auth B], WA [auth B], XA [auth B], YA [auth C], ZA [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth C] Focus chain BB [auth C] Focus chain CB [auth C] Focus chain DB [auth C] Focus chain EA [auth A] Focus chain EB [auth C] Focus chain FA [auth A] Focus chain FB [auth C] Focus chain GA [auth A] Focus chain GB [auth C] Focus chain HA [auth A] Focus chain HB [auth C] Focus chain IA [auth A] Focus chain JA [auth A] Focus chain KA [auth A] Focus chain LA [auth A] Focus chain MA [auth A] Focus chain NA [auth A] Focus chain OA [auth B] Focus chain PA [auth B] Focus chain QA [auth B] Focus chain RA [auth B] Focus chain SA [auth B] Focus chain TA [auth B] Focus chain UA [auth B] Focus chain VA [auth B] Focus chain WA [auth B] Focus chain XA [auth B] Focus chain YA [auth C] Focus chain ZA [auth C] Interactions & Density Focus chain AB [auth C] Focus chain BB [auth C] Focus chain CB [auth C] Focus chain DB [auth C] Focus chain EA [auth A] Focus chain EB [auth C] Focus chain FA [auth A] Focus chain FB [auth C] Focus chain GA [auth A] Focus chain GB [auth C] Focus chain HA [auth A] Focus chain HB [auth C] Focus chain IA [auth A] Focus chain JA [auth A] Focus chain KA [auth A] Focus chain LA [auth A] Focus chain MA [auth A] Focus chain NA [auth A] Focus chain OA [auth B] Focus chain PA [auth B] Focus chain QA [auth B] Focus chain RA [auth B] Focus chain SA [auth B] Focus chain TA [auth B] Focus chain UA [auth B] Focus chain VA [auth B] Focus chain WA [auth B] Focus chain XA [auth B] Focus chain YA [auth C] Focus chain ZA [auth C]