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Yorodumi- EMDB-26730: Structure of the human coronavirus CCoV-HuPn-2018 spike glycoprot... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26730 | |||||||||
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Title | Structure of the human coronavirus CCoV-HuPn-2018 spike glycoprotein with domain 0 in the swung out conformation | |||||||||
Map data | ||||||||||
Sample |
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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 | |||||||||
Biological species | unidentified human coronavirus / CCoV-HuPn-2018 (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||
Authors | Tortorici MA / Veesler D / Seattle Structural Genomics Center for Infectious Disease (SSGCID) | |||||||||
Funding support | United States, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_26730.map.gz | 483.9 MB | EMDB map data format | |
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Header (meta data) | emd-26730-v30.xml emd-26730.xml | 18.3 KB 18.3 KB | Display Display | EMDB header |
Images | emd_26730.png | 103.1 KB | ||
Others | emd_26730_additional_1.map.gz emd_26730_half_map_1.map.gz emd_26730_half_map_2.map.gz | 1.9 MB 474.9 MB 474.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26730 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26730 | HTTPS FTP |
-Validation report
Summary document | emd_26730_validation.pdf.gz | 841.7 KB | Display | EMDB validaton report |
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Full document | emd_26730_full_validation.pdf.gz | 841.2 KB | Display | |
Data in XML | emd_26730_validation.xml.gz | 19 KB | Display | |
Data in CIF | emd_26730_validation.cif.gz | 22.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26730 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26730 | HTTPS FTP |
-Related structure data
Related structure data | 7usaMC 7u0lC 7us6C 7us9C 7usbC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_26730.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.843 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #1
File | emd_26730_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Half map
File | emd_26730_half_map_1.map | ||||||||||||
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Annotation | Half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map
File | emd_26730_half_map_2.map | ||||||||||||
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Annotation | Half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : CCoV-HuPn-2018
Entire | Name: CCoV-HuPn-2018 (virus) |
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Components |
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-Supramolecule #1: CCoV-HuPn-2018
Supramolecule | Name: 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 |
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Host (natural) | Organism: Homo sapiens (human) |
Host system | Organism: mammal environmental sample (environmental samples) |
-Macromolecule #1: Spike glycoprotein
Macromolecule | Name: Spike glycoprotein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: unidentified human coronavirus |
Molecular weight | Theoretical: 161.621125 KDa |
Recombinant expression | Organism: mammal environmental sample (environmental samples) |
Sequence | String: 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 |
-Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 30 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Sugar embedding | Material: Tris buffer saline |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 80.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination 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 |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 70990 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |