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Yorodumi- EMDB-0056: Feline Calicivirus Strain F9 bound to a soluble ectodomain fragme... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0056 | |||||||||
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Title | Feline Calicivirus Strain F9 bound to a soluble ectodomain fragment of feline junctional adhesion molecule A - leading to assembly of a portal structure at a unique three-fold axis. | |||||||||
Map data | C3 reconstruction of Feline Calicivirus decorated with a soluble ectodomain fragment of the cellular receptor feline junctional adhesion molecule A. | |||||||||
Sample |
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Function / homology | Function and homology information establishment of endothelial intestinal barrier / regulation of membrane permeability / T=3 icosahedral viral capsid / intestinal absorption / bicellular tight junction / host cell cytoplasm / membrane => GO:0016020 / cell adhesion / plasma membrane Similarity search - Function | |||||||||
Biological species | Felis catus (domestic cat) / Feline calicivirus strain F9 / FCV (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.75 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
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_0056.map.gz | 757.7 MB | EMDB map data format | |
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Header (meta data) | emd-0056-v30.xml emd-0056.xml | 20.7 KB 20.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_0056_fsc.xml | 21 KB | Display | FSC data file |
Images | emd_0056.png | 248.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0056 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0056 | HTTPS FTP |
-Validation report
Summary document | emd_0056_validation.pdf.gz | 342.6 KB | Display | EMDB validaton report |
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Full document | emd_0056_full_validation.pdf.gz | 341.8 KB | Display | |
Data in XML | emd_0056_validation.xml.gz | 16.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0056 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0056 | HTTPS FTP |
-Related structure data
Related structure data | 6gsiMC 0054C 6gshC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | |
EM raw data | EMPIAR-10193 (Title: Calicivirus VP2 forms a portal to mediate endosome escape Data size: 867.0 Data #1: Motion corrected micrographs of feline calicivirus strain F9 decorated with feline junctional adhesion molecule A [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_0056.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | C3 reconstruction of Feline Calicivirus decorated with a soluble ectodomain fragment of the cellular receptor feline junctional adhesion molecule A. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.065 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 : Feline calicivirus strain F9
Entire | Name: Feline calicivirus strain F9 |
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Components |
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-Supramolecule #1: Feline calicivirus strain F9
Supramolecule | Name: Feline calicivirus strain F9 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 Details: Virus was propagated in Crandell Reese Feline Kidney cells Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: Felis catus (domestic cat) |
Virus shell | Shell ID: 1 / Name: Capsid / Diameter: 400.0 Å / T number (triangulation number): 3 |
-Supramolecule #2: Feline calicivirus strain F9
Supramolecule | Name: Feline calicivirus strain F9 / type: virus / ID: 2 / Parent: 1 / Macromolecule list: #1 / Details: Icosahedral Capsid / NCBI-ID: 11981 / Sci species name: Feline calicivirus strain F9 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: Felis catus (domestic cat) |
Virus shell | Shell ID: 2 / Name: Capsid / Diameter: 400.0 Å / T number (triangulation number): 3 |
-Supramolecule #3: feline junctional adhesion molecule A
Supramolecule | Name: feline junctional adhesion molecule A / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 Details: Soluble ectodomain fragment comprising Ig-like domains D1 and D2 |
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Source (natural) | Organism: Felis catus (domestic cat) |
Recombinant expression | Organism: Cricetulus griseus (Chinese hamster) / Recombinant cell: CHO cells |
-Supramolecule #4: VP2 - portal.
Supramolecule | Name: VP2 - portal. / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3 Details: Postulated to mediate endosome escape, this virion component is only present on the outer surface of the capsid following receptor engagement. |
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Source (natural) | Organism: Feline calicivirus strain F9 |
-Macromolecule #1: Capsid protein
Macromolecule | Name: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: FCV (virus) |
Molecular weight | Theoretical: 73.346664 KDa |
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 |
-Macromolecule #2: Junctional adhesion molecule A
Macromolecule | Name: Junctional adhesion molecule A / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Felis catus (domestic cat) |
Molecular weight | Theoretical: 22.18065 KDa |
Recombinant expression | Organism: Cricetulus griseus (Chinese hamster) |
Sequence | String: AVYTSEPDVR VPEDKPAKLS CSYSGFSNPR VEWKFAHGDI TSLVCYKNKI TASYADRVTF SHSGITFHSV TRKDTGTYTC MVSDDGGNT YGEVSVQLTV LVPPSKPTVH IPSSATIGSR AVLTCSEKDG SPPSEYYWFK DGVRMPLEPK GNRAFSNSSY S LNEKTGEL ...String: AVYTSEPDVR VPEDKPAKLS CSYSGFSNPR VEWKFAHGDI TSLVCYKNKI TASYADRVTF SHSGITFHSV TRKDTGTYTC MVSDDGGNT YGEVSVQLTV LVPPSKPTVH IPSSATIGSR AVLTCSEKDG SPPSEYYWFK DGVRMPLEPK GNRAFSNSSY S LNEKTGEL VFDPVSAWDT GEYTCEAQNG YGMPMRSEAV RMEA |
-Macromolecule #3: VP2
Macromolecule | Name: VP2 / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: FCV (virus) |
Molecular weight | Theoretical: 12.209838 KDa |
Sequence | String: MNSILGLIDT VTNTIGKAQQ IELDKAALGQ QRELALKRMK LDHQALNNQV EQFNKILEQR VQGPIQSVRL ARAAGFRVDP YSYTDQNFY DDQLNAIRLS YRNLFKN |
-Macromolecule #4: POTASSIUM ION
Macromolecule | Name: POTASSIUM ION / type: ligand / ID: 4 / Number of copies: 4 / 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 |
Grid | Model: C-flat-2/2 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
Details | Purified virions were incubated in the presence of purified ectodomain fragments. |
-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: 13865 / 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 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |