+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-25905 | |||||||||
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Title | Cryo-EM structure of W6 possum enterovirus | |||||||||
Map data | Enterovirus EV-F4 - isolated from Bushtail Possum | |||||||||
Sample | Enterovirus != Possum enterovirus W6 Enterovirus
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Keywords | enterovirus / icosahedral / VIRUS | |||||||||
Biological species | Possum enterovirus W6 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.96 Å | |||||||||
Authors | Wang I / Jayawardena N | |||||||||
Funding support | Canada, 1 items
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Citation | Journal: Viruses / Year: 2022 Title: Cryo-EM Structure of a Possum Enterovirus. Authors: Ivy Wang / Sandeep K Gupta / Guillaume Ems / Nadishka Jayawardena / Mike Strauss / Mihnea Bostina / Abstract: Enteroviruses (EVs) represent a substantial concern to global health. Here, we present the cryo-EM structure of a non-human enterovirus, EV-F4, isolated from the Australian brushtail possum to assess ...Enteroviruses (EVs) represent a substantial concern to global health. Here, we present the cryo-EM structure of a non-human enterovirus, EV-F4, isolated from the Australian brushtail possum to assess the structural diversity of these picornaviruses. The capsid structure, determined to ~3 Å resolution by single particle analysis, exhibits a largely smooth surface, similar to EV-F3 (formerly BEV-2). Although the cellular receptor is not known, the absence of charged residues on the outer surface of the canyon suggest a different receptor type than for EV-F3. Density for the pocket factor is clear, with the entrance to the pocket being smaller than for other enteroviruses. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_25905.map.gz | 920.6 MB | EMDB map data format | |
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Header (meta data) | emd-25905-v30.xml emd-25905.xml | 14 KB 14 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_25905_fsc.xml | 22.6 KB | Display | FSC data file |
Images | emd_25905.png | 117.4 KB | ||
Filedesc metadata | emd-25905.cif.gz | 5.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-25905 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25905 | HTTPS FTP |
-Validation report
Summary document | emd_25905_validation.pdf.gz | 753.4 KB | Display | EMDB validaton report |
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Full document | emd_25905_full_validation.pdf.gz | 753 KB | Display | |
Data in XML | emd_25905_validation.xml.gz | 18.4 KB | Display | |
Data in CIF | emd_25905_validation.cif.gz | 25.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25905 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25905 | HTTPS FTP |
-Related structure data
Related structure data | 7thxMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_25905.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Enterovirus EV-F4 - isolated from Bushtail Possum | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.857 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Enterovirus
Entire | Name: Enterovirus |
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Components |
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-Supramolecule #1: Possum enterovirus W6
Supramolecule | Name: Possum enterovirus W6 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 / NCBI-ID: 263532 / Sci species name: Possum enterovirus W6 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: Possum enterovirus W6 |
-Macromolecule #1: Capsid protein VP1
Macromolecule | Name: Capsid protein VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Possum enterovirus W6 |
Molecular weight | Theoretical: 30.311832 KDa |
Sequence | String: GETGQLIKDT IKNTVENTVE STHSISTEAT PALQAAETGA TSNASDESMI ETRNVVNTHG VAETSLEGFY GRAGLVAMFT TEGGIRSWY INFGKYVQLR AKLELLTYAR FDVEFTIVAQ VVDEQAKVKD FNVDYQVMYV PPGASAPDGQ DSFQWQSSCN P SVISNTGL ...String: GETGQLIKDT IKNTVENTVE STHSISTEAT PALQAAETGA TSNASDESMI ETRNVVNTHG VAETSLEGFY GRAGLVAMFT TEGGIRSWY INFGKYVQLR AKLELLTYAR FDVEFTIVAQ VVDEQAKVKD FNVDYQVMYV PPGASAPDGQ DSFQWQSSCN P SVISNTGL PPARVSVPFM SSANAYSFSY DGYIQFGDTS SSSYGILPIH YLGQLVVRTC EDLDSARLRV RIYAKPKHMR GW IPRSPRM RPYVSRFTGI YTDAPSFCVN RESITTAG |
-Macromolecule #2: Capsid protein VP2
Macromolecule | Name: Capsid protein VP2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Possum enterovirus W6 |
Molecular weight | Theoretical: 26.577887 KDa |
Sequence | String: SAEACGYSDR VAQLTLGNST ITTQEAANIV VAYGRWPSGL RDTDATAVDK PTQPGVSAER FYTLPSVQWT TSFTGHYWKL PDALSDLGL FGQNLQFHYL YRGGWAIHVQ CNATKFHQGT LLVVAVPEHK IQAQSNPSFG RTNPGEAGAA CQFPFTFEDG T ALGNALIY ...String: SAEACGYSDR VAQLTLGNST ITTQEAANIV VAYGRWPSGL RDTDATAVDK PTQPGVSAER FYTLPSVQWT TSFTGHYWKL PDALSDLGL FGQNLQFHYL YRGGWAIHVQ CNATKFHQGT LLVVAVPEHK IQAQSNPSFG RTNPGEAGAA CQFPFTFEDG T ALGNALIY PHQWINLRTN NSATLVLPYV NAIPMDSGIK HNNWTLLVIP IVPLEYAVGA TTFVPITVTI APMCTEYNGL RA AVTQ |
-Macromolecule #3: Capsid protein VP3
Macromolecule | Name: Capsid protein VP3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Possum enterovirus W6 |
Molecular weight | Theoretical: 26.997758 KDa |
Sequence | String: GCPTLYTPGS GQFLTTDDFQ TPCMLPKFQP TPVIDIPGEV KNFLEVIQVE SLVEINNVSG VEGVARYRIP LNVQDAMDGQ IMAVRVDPG ADGPMQSTLL GVFTRYYTQW SGSLDFTFMF CGTFMTTGKV IIAYTPPGGD QPGSRQQAML GTHVVWDFGL Q SSITLVVP ...String: GCPTLYTPGS GQFLTTDDFQ TPCMLPKFQP TPVIDIPGEV KNFLEVIQVE SLVEINNVSG VEGVARYRIP LNVQDAMDGQ IMAVRVDPG ADGPMQSTLL GVFTRYYTQW SGSLDFTFMF CGTFMTTGKV IIAYTPPGGD QPGSRQQAML GTHVVWDFGL Q SSITLVVP WISSGHFRGT SLDNTIYKYR YYEAGYITMW YQTNMVVPPN FPTEASILMF VAAQPNFSLR ILKDRPDITQ VA SLQ |
-Macromolecule #4: Capsid protein VP4
Macromolecule | Name: Capsid protein VP4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Possum enterovirus W6 |
Molecular weight | Theoretical: 7.63234 KDa |
Sequence | String: MGAQLSKNTA GSHTTGTYAT GGSSIHYTNI NYYENAASNS LNKQDFTQDP DKFTRPVADI MKEAAVPLKS P |
-Macromolecule #5: SPHINGOSINE
Macromolecule | Name: SPHINGOSINE / type: ligand / ID: 5 / Number of copies: 1 / Formula: SPH |
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Molecular weight | Theoretical: 299.492 Da |
Chemical component information | ChemComp-SPH: |
-Macromolecule #6: POTASSIUM ION
Macromolecule | Name: POTASSIUM ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: K |
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Molecular weight | Theoretical: 39.098 Da |
-Macromolecule #7: water
Macromolecule | Name: water / type: ligand / ID: 7 / Number of copies: 21 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.37 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: 3.0 µm / Nominal defocus min: 0.75 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |