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- EMDB-26729: CCoV-HuPn-2018 S in the proximal conformation (local refinement o... -

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Basic information

Entry
Database: EMDB / ID: EMD-26729
TitleCCoV-HuPn-2018 S in the proximal conformation (local refinement of domain 0)
Map data
Sample
  • Virus: CCoV-HuPn-2018 (virus)
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHuman coronavirus / Coronavirus / CCoV-HuPn-2018 / spike glycoprotein / Alpha-coronaviruses / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / VIRAL PROTEIN
Function / homology
Function and homology information


endocytosis involved in viral entry into host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion membrane / membrane
Similarity search - Function
Spike glycoprotein, Alphacoronavirus / Spike glycoprotein S1, coronavirus / Coronavirus spike glycoprotein S1 / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. ...Spike glycoprotein, Alphacoronavirus / Spike glycoprotein S1, coronavirus / Coronavirus spike glycoprotein S1 / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Biological speciesunidentified human coronavirus / CCoV-HuPn-2018 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsTortorici MA / Veesler D
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Cell / Year: 2022
Title: Structure, receptor recognition, and antigenicity of the human coronavirus CCoV-HuPn-2018 spike glycoprotein.
Authors: M Alejandra Tortorici / Alexandra C Walls / Anshu Joshi / Young-Jun Park / Rachel T Eguia / Marcos C Miranda / Elizabeth Kepl / Annie Dosey / Terry Stevens-Ayers / Michael J Boeckh / Amalio ...Authors: M Alejandra Tortorici / Alexandra C Walls / Anshu Joshi / Young-Jun Park / Rachel T Eguia / Marcos C Miranda / Elizabeth Kepl / Annie Dosey / Terry Stevens-Ayers / Michael J Boeckh / Amalio Telenti / Antonio Lanzavecchia / Neil P King / Davide Corti / Jesse D Bloom / David Veesler /
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- ...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.
History
DepositionApr 23, 2022-
Header (metadata) releaseAug 24, 2022-
Map releaseAug 24, 2022-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26729.png

Downloads & links

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Map

FileDownload / File: emd_26729.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 512 pix.
= 431.616 Å		0.84 Å/pix.
x 512 pix.
= 431.616 Å		0.84 Å/pix.
x 512 pix.
= 431.616 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.843 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.833
Minimum - Maximum-4.297736 - 7.4809027
Average (Standard dev.)0.0001750076 (±0.018597094)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 431.616 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_26729_additional_1.map
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Half map: #2

Fileemd_26729_half_map_1.map
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Half map: #1

Fileemd_26729_half_map_2.map
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Sample components

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Entire : CCoV-HuPn-2018

EntireName: CCoV-HuPn-2018 (virus)
Components
  • Virus: CCoV-HuPn-2018 (virus)
    • Protein or peptide: Spike glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: CCoV-HuPn-2018

SupramoleculeName: CCoV-HuPn-2018 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 2697049 / Sci species name: CCoV-HuPn-2018 / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: Yes / Virus empty: Yes
Host (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: unidentified human coronavirus
Molecular weightTheoretical: 29.960043 KDa
Recombinant expressionOrganism: mammal environmental sample (environmental samples)
SequenceString: MGILPSPGMP ALLSLVSLLS VLLMGCVAET GTDNFPCSKF LNRTIGNHWN LIENFLLNYS IRLPPNSDVV LGDYFPTVQP WFNCIRNNN NSLYVTMENL KALYWDYATE NITSDHRQRL HVVVKGKPYS ITVTTTRNFD AAEGAIICIC KGSPPTTTTG N LDCNWGSD ...String:
MGILPSPGMP ALLSLVSLLS VLLMGCVAET GTDNFPCSKF LNRTIGNHWN LIENFLLNYS IRLPPNSDVV LGDYFPTVQP WFNCIRNNN NSLYVTMENL KALYWDYATE NITSDHRQRL HVVVKGKPYS ITVTTTRNFD AAEGAIICIC KGSPPTTTTG N LDCNWGSD CRLNHKFPIC PSNSQANCGN MLYGLQWFTD EVVAYLHGAI YRISFENKWF GTVTLGDMRA TTLQTAGALV DL WWFNPVY DVTYYRVNNK NGTTIVSNCT

UniProtKB: Spike glycoprotein

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 2 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
Sugar embeddingMaterial: Tris buffer saline
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 80.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5szs

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 36141
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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