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- EMDB-26727: Structure of the human coronavirus CCoV-HuPn-2018 spike glycoprot... -

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Basic information

Entry
Database: EMDB / ID: EMD-26727
TitleStructure of the human coronavirus CCoV-HuPn-2018 spike glycoprotein with domain 0 in the proximal conformation
Map data
Sample
  • Virus: unidentified human coronavirus
    • Protein or peptide: Spike glycoproteinSpike protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
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 / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus ...Spike glycoprotein, Alphacoronavirus / Spike glycoprotein S1, coronavirus / Coronavirus spike glycoprotein S1 / Spike glycoprotein S2, coronavirus, C-terminal / Coronavirus spike glycoprotein S2, intravirion / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 2 (HR2) region profile. / Coronavirus spike (S) glycoprotein S2 subunit heptad repeat 1 (HR1) region profile. / Spike glycoprotein S2 superfamily, coronavirus / Spike glycoprotein S2, coronavirus / Coronavirus spike glycoprotein S2 / Coronavirus spike glycoprotein S1, C-terminal / Coronavirus spike glycoprotein S1, C-terminal
Similarity search - Domain/homology
Biological speciesunidentified human coronavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsTortorici MA / Veesler D / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
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-
UpdateAug 24, 2022-
Current statusAug 24, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26727.png

Downloads & links

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Map

FileDownload / File: emd_26727.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
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: 0.668
Minimum - Maximum-2.0699565 - 3.4103544
Average (Standard dev.)-0.00021279664 (±0.066443086)
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_26727_additional_1.map
Projections & Slices
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Half map: #2

Fileemd_26727_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_26727_half_map_2.map
Projections & Slices
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Sample components

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Entire : unidentified human coronavirus

EntireName: unidentified human coronavirus
Components
  • Virus: unidentified human coronavirus
    • Protein or peptide: Spike glycoproteinSpike protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: unidentified human coronavirus

SupramoleculeName: unidentified human coronavirus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 694448 / Sci species name: unidentified human coronavirus / Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: Yes / Virus empty: Yes
Host (natural)Organism: Homo sapiens (human)
Host systemOrganism: mammal environmental sample (environmental samples)

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Macromolecule #1: Spike glycoprotein

MacromoleculeName: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: unidentified human coronavirus
Molecular weightTheoretical: 142.666391 KDa
Recombinant expressionOrganism: mammal environmental sample (environmental samples)
SequenceString: HWNLIENFLL NYSIRLPPNS DVVLGDYFPT VQPWFNCIRN NNNSLYVTME NLKALYWDYA TENITSDHRQ PVYDVTYYRV NNKNGTTIV SNCTDQCASY VDNVFTTQPG GLIPSDFSFN NWFLLTNSST VVSGKLVTRQ PLVVNCLWPV PSFKEAASTF C FEGAGFDQ ...String:
HWNLIENFLL NYSIRLPPNS DVVLGDYFPT VQPWFNCIRN NNNSLYVTME NLKALYWDYA TENITSDHRQ PVYDVTYYRV NNKNGTTIV SNCTDQCASY VDNVFTTQPG GLIPSDFSFN NWFLLTNSST VVSGKLVTRQ PLVVNCLWPV PSFKEAASTF C FEGAGFDQ CNGAVLNNTV DVIRFNLNFT ADVQSGMGAT VFSLNTTGGV ILEISCYNDI VSESSFYSYG DIPFGITDGP RY CYVLYNG TTLKYLGTLP PSVKEIAISK WGHFYINGYN FFSTFPIDCI SFNLTTGASG AFWTIAYTSY TEALVQVENT AIK KVTYCN SHINNIKCSQ LTANLQNGFY PVASSEVGLV NKSVVLLPSF FAHTTVNITI DLGMKRSGYG QPIASPLSNI TLPM QDNNT DVYCIRSNQF SIYVHSTCKS SLWDNVFNQD CTDVLEATAV IKTGTCPFSF DKLNNHLTFN KFCLSLSPVG ANCKF DVAA RTRTNEQVVR SLYVIYEEGD NIVGVPSDNS GLHDLSVLHL DSCTDYNIYG RTGVGVIRQT NSTLLSGLYY TSLSGD LLG FKNVSDGVIY SVTPCDVSAQ AAVIDGAIVG AMTSINSELL GLTHWTTTPN FYYYSIYNYT NERTRGTAID SNDVDCE PI ITYSNIGVCK NGALVFINVT HSDGDVQPIS TGNVTIPTNF TISVQVEYIQ VYTTPVSIDC ARYVCNGNPR CNKLLTQY V SACQTIEQAL AMGARLENME VDSMLFVSEN ALKLASVEAF NSTENLDPIY KEWPNIGGSW LGGLKDILPS HNSKRKYRS AIEDLLFDKV VTSGLGTVDE DYKRCTGGYD IADLVCAQYY NGIMVLPGVA NDDKMTMYTA SLAGGITLGA LGGGAVAIPF AVAVQARLN YVALQTDVLN KNQQILANAF NQAIGNITQA FGKVNDAIHQ TSKGLATVAK VLAKVQDVVN TQGQALSHLT V QLQNNFQA ISSSISDIYN RLDPPSADAQ VDRLITGRLT ALNAFVSQTL TRQAEVRASR QLAKDKVNEC VRSQSQRFGF CG NGTHLFS LANAAPNGMI FFHTVLLPTA YQTVTACSGI CASDGDRTFG LVVKDVQLTL FRNLDDKFYL TPRTMYQPRA ATS SDFVQI EGCDVLFVNA TEIDLPSIIP DYIDINQTVQ DILENYRPNW TVPELTLDIF NATYLNLTGE IDDLEFRSEK LHNT TVELA ILIDNINNTL VNLEWLNRIE TYVKSGGYIP EAPRDGQAYV RKDGEWVLLS TFLVPRGSGG SGGSGLNDIF EAQKI EWHE GGSHHHHHHH H

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 43 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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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: protein
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.8 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 80.0 e/Å2
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

Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 38863

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