+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0054 | |||||||||
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Title | Feline Calicivirus Strain F9 | |||||||||
Map data | Icosahedral reconstruction of feline calicivirus strain F9 | |||||||||
Sample |
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Keywords | Capsid / Calicivirus / Vesivirus / Vp1 / VIRUS | |||||||||
Function / homology | T=3 icosahedral viral capsid / Calicivirus coat protein / Calicivirus coat protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Capsid protein VP1 Function and homology information | |||||||||
Biological species | Feline calicivirus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
Authors | Conley MJ / Bhella D | |||||||||
Funding support | United Kingdom, 2 items
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Citation | Journal: Nature / Year: 2019 Title: Calicivirus VP2 forms a portal-like assembly following receptor engagement. Authors: Michaela J Conley / Marion McElwee / Liyana Azmi / Mads Gabrielsen / Olwyn Byron / Ian G Goodfellow / David Bhella / Abstract: To initiate infection, many viruses enter their host cells by triggering endocytosis following receptor engagement. However, the mechanisms by which non-enveloped viruses escape the endosome are ...To initiate infection, many viruses enter their host cells by triggering endocytosis following receptor engagement. However, the mechanisms by which non-enveloped viruses escape the endosome are poorly understood. Here we present near-atomic-resolution cryo-electron microscopy structures for feline calicivirus both undecorated and labelled with a soluble fragment of its cellular receptor, feline junctional adhesion molecule A. We show that VP2, a minor capsid protein encoded by all caliciviruses, forms a large portal-like assembly at a unique three-fold axis of symmetry, following receptor engagement. This assembly-which was not detected in undecorated virions-is formed of twelve copies of VP2, arranged with their hydrophobic N termini pointing away from the virion surface. Local rearrangement at the portal site leads to the opening of a pore in the capsid shell. We hypothesize that the portal-like assembly functions as a channel for the delivery of the calicivirus genome, through the endosomal membrane, into the cytoplasm of a host cell, thereby initiating infection. VP2 was previously known to be critical for the production of infectious virus; our findings provide insights into its structure and function that advance our understanding of the Caliciviridae. | |||||||||
History |
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-Structure visualization
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
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Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_0054.map.gz | 480.3 MB | EMDB map data format | |
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Header (meta data) | emd-0054-v30.xml emd-0054.xml | 12.8 KB 12.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_0054_fsc.xml | 17.5 KB | Display | FSC data file |
Images | emd_0054.png | 226.5 KB | ||
Filedesc metadata | emd-0054.cif.gz | 6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0054 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0054 | HTTPS FTP |
-Validation report
Summary document | emd_0054_validation.pdf.gz | 274.3 KB | Display | EMDB validaton report |
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Full document | emd_0054_full_validation.pdf.gz | 273.5 KB | Display | |
Data in XML | emd_0054_validation.xml.gz | 15.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0054 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0054 | HTTPS FTP |
-Related structure data
Related structure data | 6gshMC 0056C 6gsiC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10192 (Title: Calicivirus VP2 forms a portal to mediate endosome escape Data size: 324.9 Data #1: Motion corrected micrographs of feline calicivirus strain F9 [micrographs - single frame]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_0054.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Icosahedral reconstruction of feline calicivirus strain F9 | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.065 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : T=3 Icosahedral Capsid.
Entire | Name: T=3 Icosahedral Capsid. |
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Components |
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-Supramolecule #1: T=3 Icosahedral Capsid.
Supramolecule | Name: T=3 Icosahedral Capsid. / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: T=3 Icosahedral Capsid |
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Source (natural) | Organism: Feline calicivirus |
-Macromolecule #1: VP1
Macromolecule | Name: VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Feline calicivirus |
Molecular weight | Theoretical: 73.346664 KDa |
Recombinant expression | Organism: Felis catus (domestic cat) |
Sequence | String: MCSTCANVLK YYNWDPHFRL VIDPNKFLSV GFCDNPLMCC YPELLPEFGT VWDCDQSPLQ IYLESILGDD EWASTYEAID PAVPPMHWD AAGKIFQPHP GVLMHHLIGE VAKAWDPNLP MFRLEADGDG SITAPEQGTP VGGVIAEPSA QMSAAADMAT G KSVDSEWE ...String: MCSTCANVLK YYNWDPHFRL VIDPNKFLSV GFCDNPLMCC YPELLPEFGT VWDCDQSPLQ IYLESILGDD EWASTYEAID PAVPPMHWD AAGKIFQPHP GVLMHHLIGE VAKAWDPNLP MFRLEADGDG SITAPEQGTP VGGVIAEPSA QMSAAADMAT G KSVDSEWE AFFSFHTSVN WSTSETQGKI LFKQSLGPLL NPYLEHLAKL YVAWSGSIDV RFSISGSGVF GGKLAAIVVP PG VDPVQST SMLQYPHVLF DARQVEPVIF SIPDLRSTLY HLMSDTDTTS LVIMVYNDLI NPYANDSNSS GCIVTVETKP GAD FKFHLL KPPGSMLTHG SVPSDLIPKS SSLWIGNRHW TDITDFVIRP FVFQANRHFD FNQETAGWST PRYRPITITI SEKN GAKLG IGVATDYIVP GIPDGWPDTT IPEKLTPAGD YAITNKSGND ITTAAGYDGA DVIVNNTNFK GMYICGSLQR AWGDK KISN TAFITTATKV DNAIEPSNVI DMTKIAVYQD THVGKEVQTS DDTLSLLGYT GIGEQAIGSD RDRVVRISVL PETGAR GGN HPIFYKNSIK LGYVIRSIDV FNSQILHTSR QLSLNHYLLP PDSFAVYRII DSNGSWFDIG IDSDGFSFVG VSSIGKL EF PLTASYMGIQ LAKIRLASNI RSSMTKL UniProtKB: Capsid protein VP1 |
-Macromolecule #2: POTASSIUM ION
Macromolecule | Name: POTASSIUM ION / type: ligand / ID: 2 / Number of copies: 3 / Formula: K |
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Molecular weight | Theoretical: 39.098 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 7.2 / Details: Phosphate buffered saline |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
Details | Purified enveloped virions |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 1 / Number real images: 5198 / Average electron dose: 63.0 e/Å2 Details: Each micrograph was recorded as a movie of 50 individual fractions with a total dose of 63 e/angstrom squared |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 75000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |