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- EMDB-26730: Structure of the human coronavirus CCoV-HuPn-2018 spike glycoprot... -

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Basic information

Entry
Database: EMDB / ID: EMD-26730
TitleStructure of the human coronavirus CCoV-HuPn-2018 spike glycoprotein with domain 0 in the swung out conformation
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


host cell endoplasmic reticulum-Golgi intermediate compartment membrane / receptor-mediated virion attachment to host cell / 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 / 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 superfamily, coronavirus / Spike glycoprotein S2, coronavirus, heptad repeat 1 / Spike glycoprotein S2, coronavirus, heptad repeat 2 ...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 superfamily, coronavirus / 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, coronavirus / Coronavirus spike glycoprotein S2
Similarity search - Domain/homology
Biological speciesunidentified human coronavirus / CCoV-HuPn-2018 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 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-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26730.png

Downloads & links

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Map

FileDownload / File: emd_26730.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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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: 0.706
Minimum - Maximum-3.135606 - 4.425129
Average (Standard dev.)-0.00028396043 (±0.0846838)
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_26730_additional_1.map
Projections & Slices
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Half map: Half map

Fileemd_26730_half_map_1.map
AnnotationHalf map
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Half map: Half map

Fileemd_26730_half_map_2.map
AnnotationHalf 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: 3 / Enantiomer: LEVO
Source (natural)Organism: unidentified human coronavirus
Molecular weightTheoretical: 161.621125 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 DQCASYVDNV FTTQPGGLIP SDFSFNNWFL LTNSSTVVSG KLVTRQPLVV NCL WPVPSF KEAASTFCFE GAGFDQCNGA VLNNTVDVIR FNLNFTADVQ SGMGATVFSL NTTGGVILEI SCYNDIVSES SFYS YGDIP FGITDGPRYC YVLYNGTTLK YLGTLPPSVK EIAISKWGHF YINGYNFFST FPIDCISFNL TTGASGAFWT IAYTS YTEA LVQVENTAIK KVTYCNSHIN NIKCSQLTAN LQNGFYPVAS SEVGLVNKSV VLLPSFFAHT TVNITIDLGM KRSGYG QPI ASPLSNITLP MQDNNTDVYC IRSNQFSIYV HSTCKSSLWD NVFNQDCTDV LEATAVIKTG TCPFSFDKLN NHLTFNK FC LSLSPVGANC KFDVAARTRT NEQVVRSLYV IYEEGDNIVG VPSDNSGLHD LSVLHLDSCT DYNIYGRTGV GVIRQTNS T LLSGLYYTSL SGDLLGFKNV SDGVIYSVTP CDVSAQAAVI DGAIVGAMTS INSELLGLTH WTTTPNFYYY SIYNYTNER TRGTAIDSND VDCEPIITYS NIGVCKNGAL VFINVTHSDG DVQPISTGNV TIPTNFTISV QVEYIQVYTT PVSIDCARYV CNGNPRCNK LLTQYVSACQ TIEQALAMGA RLENMEVDSM LFVSENALKL ASVEAFNSTE NLDPIYKEWP NIGGSWLGGL K DILPSHNS KRKYRSAIED LLFDKVVTSG LGTVDEDYKR CTGGYDIADL VCAQYYNGIM VLPGVANDDK MTMYTASLAG GI TLGALGG GAVAIPFAVA VQARLNYVAL QTDVLNKNQQ ILANAFNQAI GNITQAFGKV NDAIHQTSKG LATVAKVLAK VQD VVNTQG QALSHLTVQL QNNFQAISSS ISDIYNRLDP PSADAQVDRL ITGRLTALNA FVSQTLTRQA EVRASRQLAK DKVN ECVRS QSQRFGFCGN GTHLFSLANA APNGMIFFHT VLLPTAYQTV TACSGICASD GDRTFGLVVK DVQLTLFRNL DDKFY LTPR TMYQPRAATS SDFVQIEGCD VLFVNATEID LPSIIPDYID INQTVQDILE NYRPNWTVPE LTLDIFNATY LNLTGE IDD LEFRSEKLHN TTVELAILID NINNTLVNLE WLNRIETYVK SGGYIPEAPR DGQAYVRKDG EWVLLSTFLV PRGSGGS GG SGLNDIFEAQ KIEWHEGGSH HHHHHHH

UniProtKB: Spike glycoprotein

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 30 / 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: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 70990
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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