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- EMDB-12194: The cryo-EM structure of vesivirus 2117, an adventitious agent an... -

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Basic information

Entry
Database: EMDB / ID: EMD-12194
TitleThe cryo-EM structure of vesivirus 2117, an adventitious agent and possible cause of haemorrhagic gastroenteritis in dogs.
Map dataVesivirus 2117 virus-like particle - sharpened map
Sample
  • Virus: Calicivirus isolate 2117
    • Protein or peptide: Capsid proteinCapsid
Keywordscapsid / calicivirus / vp1 / VIRAL PROTEIN
Function / homologyT=3 icosahedral viral capsid / Calicivirus coat protein / Calicivirus coat protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / host cell cytoplasm / cytoplasm / Capsid protein
Function and homology information
Biological speciesCalicivirus isolate 2117
Methodsingle particle reconstruction / cryo EM / Resolution: 3.65 Å
AuthorsSutherland H / Conley MJ
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UU_12014/7 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/T002239/1 United Kingdom
Citation
Journal: J Virol / Year: 2021
Title: The Cryo-EM Structure of Vesivirus 2117 Highlights Functional Variations in Entry Pathways for Viruses in Different Clades of the Genus.
Authors: Hazel Sutherland / Michaela J Conley / Edward Emmott / James Streetley / Ian G Goodfellow / David Bhella /
Abstract: Vesivirus 2117 is an adventitious agent that has been responsible for lost productivity in biopharmaceutical production following contamination of Chinese hamster ovary cell cultures in commercial ...Vesivirus 2117 is an adventitious agent that has been responsible for lost productivity in biopharmaceutical production following contamination of Chinese hamster ovary cell cultures in commercial bioreactors. A member of the , 2117 is classified within the Vesivirus genus in a clade that includes canine and mink caliciviruses but is distinct from the vesicular exanthema of swine virus (VESV) clade, which includes the extensively studied feline calicivirus (FCV). We have used cryogenic electron microscopy (cryo-EM) to determine the structure of the capsid of this small, icosahedral, positive-sense-RNA-containing virus. We show that the outer face of the dimeric capsomeres, which contains the receptor binding site and major immunodominant epitopes in all caliciviruses studied thus far, is quite different from that of FCV. This is a consequence of a 22-amino-acid insertion in the sequence of the FCV major capsid protein that forms a "cantilevered arm" that both plays an important role in receptor engagement and undergoes structural rearrangements thought to be important for genome delivery to the cytosol. Our data highlight a potentially important difference in the attachment and entry pathways employed by the different clades of the genus. Vesivirus 2117 has caused significant losses in manufacturing of biopharmaceutical products following contamination of cell cultures used in their production. We report the structure of the vesivirus 2117 capsid, the shell that encloses the virus's genome. Comparison of this structure with that of a related vesivirus, feline calicivirus (FCV), highlighted potentially important differences related to virus attachment and entry. Our findings suggest that these two viruses may bind differently to receptors at the host cell surface. We also show that a region of the capsid protein of FCV that rearranges following receptor engagement is not present in vesivirus 2117. These structural changes in the FCV capsid have been shown to allow the assembly of a portal-like structure that is hypothesized to deliver the viral genome to the cell's interior. Our data suggest that the 2117 portal assembly may employ a different means of anchoring to the outer face of the capsid.
#1: Journal: Biorxiv / Year: 2021
Title: The cryo-EM structure of vesivirus 2117 highlights functional variations in entry pathways for viruses in different clades of the Vesivirus genus
Authors: Sutherland H / Conley MJ / Emmott E / Streetley J / Goodfellow IG / Bhella D
History
DepositionJan 14, 2021-
Header (metadata) releaseApr 14, 2021-
Map releaseApr 14, 2021-
UpdateMay 1, 2024-
Current statusMay 1, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.012
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.012
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7bjp
  • Surface level: 0.012
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7bjp
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12194.png

Downloads & links

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Map

FileDownload / File: emd_12194.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationVesivirus 2117 virus-like particle - sharpened map
Voxel sizeX=Y=Z: 0.998 Å
Density
Contour LevelBy AUTHOR: 0.012 / Movie #1: 0.012
Minimum - Maximum-0.027100747 - 0.046640877
Average (Standard dev.)-0.00003600447 (±0.0038330227)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 510.976 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.9980.9980.998
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z510.976510.976510.976
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-0.0270.047-0.000

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Supplemental data

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Additional map: Vesivirus 2117 virus-like particle - DeepEMhancer modified map

Fileemd_12194_additional_1.map
AnnotationVesivirus 2117 virus-like particle - DeepEMhancer modified map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Calicivirus isolate 2117

EntireName: Calicivirus isolate 2117
Components
  • Virus: Calicivirus isolate 2117
    • Protein or peptide: Capsid proteinCapsid

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Supramolecule #1: Calicivirus isolate 2117

SupramoleculeName: Calicivirus isolate 2117 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all
Details: The major capsid protein VP1 was expressed in a baculovirus system - in Hi5 cells
NCBI-ID: 241631 / Sci species name: Calicivirus isolate 2117 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: unidentified (others)
Virus shellShell ID: 1 / Name: VP1 / Diameter: 400.0 Å / T number (triangulation number): 3

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Macromolecule #1: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Calicivirus isolate 2117
Molecular weightTheoretical: 58.40282 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSGDASSGSP DITGEEQGVA VATGTQPSAP AMATLATAAT GTMPEEWKTF FSYYTTVNWS TTDETGKVLF VQGLSPRMNP FLDHLAKMY TGWSGSMEIR FTISGSGVFG GKLAAVMVPP GIGTEGGTSL LQFPHVLVDA RQTEPVIFNI PDIRTVLWHD M HDTLTAHL ...String:
MSGDASSGSP DITGEEQGVA VATGTQPSAP AMATLATAAT GTMPEEWKTF FSYYTTVNWS TTDETGKVLF VQGLSPRMNP FLDHLAKMY TGWSGSMEIR FTISGSGVFG GKLAAVMVPP GIGTEGGTSL LQFPHVLVDA RQTEPVIFNI PDIRTVLWHD M HDTLTAHL VILVYNDLLN PYQNTTTGTS CTVTVETRGG TDFEFHLLKP PSRKMIFGAD PSRLIPKKSM FWEGNRLPGE FK GFSIKPL VFQANRHFDC KRQTFGWSTP EHAGVKLNIQ RQNLDTEDKT DIGVHLVTGL KTIKSQVPDG WPDYYGRNII LAN TTASFG EVSEAMLGTV VPYRVSGKLE WRHLPEIAFA NGTAKNSTIV CGKYLTGNFY VGGNFTQQGN VVVYPAFWTS KHGD TKCIG EDEDMVKRID VLPQAQTTGG NYPIYYVTEF PAAYLPAPRV YNSQLLWTSR LLAQDVYDIG PEALAVFKIK DSAGN WFDI GISCEGFSFV GAPTLPFSSL QFPLEASYVG MASAYNKLQH NIAGTSVTL

UniProtKB: Capsid protein

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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

Concentration0.2 mg/mL
BufferpH: 7.4 / Details: Phosphate buffered saline
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: Sample was loaded onto C-flat C1.2/1.3 grids bearing a thin continuous carbon film, allowed to adsorb for one minute before blotting for 3 seconds and plunging into liquid ethane..
DetailsVirus-like particles

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Sample stageSpecimen holder model: JEOL CRYOSPECPORTER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: DIRECT ELECTRON DE-64 (8k x 8k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 8192 pixel / Digitization - Dimensions - Height: 8192 pixel / Digitization - Frames/image: 1-50 / Number grids imaged: 5 / Number real images: 2000 / Average exposure time: 2.0 sec. / Average electron dose: 55.0 e/Å2
Details: Data collection was performed as part of installation of the new CryoARM 300 microscope - five short sessions were run using primarily JADAS although one collection was performed using SerialEM.

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Image processing

Particle selectionNumber selected: 65071
Details: Automated particle picking was performed using RELION
Startup modelType of model: EMDB MAP
EMDB ID:

0056

Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 3.0.3) / Details: RELION 3D classification
Final 3D classificationNumber classes: 3 / Software - Name: RELION (ver. 3.0.3)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 3.0.3) / Details: RELION Refine3D
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.65 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.3) / Number images used: 15989
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-7bjp:
The cryo-EM structure of vesivirus 2117, an adventitious agent and possible cause of haemorrhagic gastroenteritis in dogs.

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