+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22008 | |||||||||
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Title | The Cutavirus (CuV) capsid structure | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Icosahedral Capsid / Cutavirus / CuV / VIRUS / Protoparvovirus | |||||||||
Function / homology | Function and homology information symbiont entry into host cell via permeabilization of inner membrane / permeabilization of host organelle membrane involved in viral entry into host cell / T=1 icosahedral viral capsid / clathrin-dependent endocytosis of virus by host cell / virion attachment to host cell / structural molecule activity Similarity search - Function | |||||||||
Biological species | Cutavirus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.87 Å | |||||||||
Authors | Mietzsch M / Agbandje-McKenna M | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Viruses / Year: 2020 Title: Structural Characterization of Cuta- and Tusavirus: Insight into Protoparvoviruses Capsid Morphology. Authors: Mario Mietzsch / Robert McKenna / Elina Väisänen / Jennifer C Yu / Maria Ilyas / Joshua A Hull / Justin Kurian / J Kennon Smith / Paul Chipman / Yi Lasanajak / David Smith / Maria ...Authors: Mario Mietzsch / Robert McKenna / Elina Väisänen / Jennifer C Yu / Maria Ilyas / Joshua A Hull / Justin Kurian / J Kennon Smith / Paul Chipman / Yi Lasanajak / David Smith / Maria Söderlund-Venermo / Mavis Agbandje-McKenna / Abstract: Several members of the genus, capable of infecting humans, have been recently discovered, including cutavirus (CuV) and tusavirus (TuV). To begin the characterization of these viruses, we have used ...Several members of the genus, capable of infecting humans, have been recently discovered, including cutavirus (CuV) and tusavirus (TuV). To begin the characterization of these viruses, we have used cryo-electron microscopy and image reconstruction to determine their capsid structures to ~2.9 Å resolution, and glycan array and cell-based assays to identify glycans utilized for cellular entry. Structural comparisons show that the CuV and TuV capsids share common features with other parvoviruses, including an eight-stranded anti-parallel β-barrel, depressions at the icosahedral 2-fold and surrounding the 5-fold axes, and a channel at the 5-fold axes. However, the viruses exhibit significant topological differences in their viral protein surface loops. These result in three separated 3-fold protrusions, similar to the bufaviruses also infecting humans, suggesting a host-driven structure evolution. The surface loops contain residues involved in receptor binding, cellular trafficking, and antigenic reactivity in other parvoviruses. In addition, terminal sialic acid was identified as the glycan potentially utilized by both CuV and TuV for cellular entry, with TuV showing additional recognition of poly-sialic acid and sialylated Lewis X (sLeXLeXLeX) motifs reported to be upregulated in neurotropic and cancer cells, respectively. These structures provide a platform for annotating the cellular interactions of these human pathogens. | |||||||||
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_22008.map.gz | 263 MB | EMDB map data format | |
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Header (meta data) | emd-22008-v30.xml emd-22008.xml | 10.1 KB 10.1 KB | Display Display | EMDB header |
Images | emd_22008.png | 315.7 KB | ||
Filedesc metadata | emd-22008.cif.gz | 5.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22008 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22008 | HTTPS FTP |
-Validation report
Summary document | emd_22008_validation.pdf.gz | 709.9 KB | Display | EMDB validaton report |
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Full document | emd_22008_full_validation.pdf.gz | 709.5 KB | Display | |
Data in XML | emd_22008_validation.xml.gz | 7.7 KB | Display | |
Data in CIF | emd_22008_validation.cif.gz | 8.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22008 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22008 | HTTPS FTP |
-Related structure data
Related structure data | 6x2iMC 6x2kC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_22008.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.057 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 : Cutavirus
Entire | Name: Cutavirus |
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Components |
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-Supramolecule #1: Cutavirus
Supramolecule | Name: Cutavirus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 1867125 / Sci species name: Cutavirus / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No |
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-Macromolecule #1: VP2
Macromolecule | Name: VP2 / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO |
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Source (natural) | Organism: Cutavirus |
Molecular weight | Theoretical: 61.252547 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: GSGVGHSTGD YNNRTEFIYH GDEVTIICHS TRLVHINMSD REDYIIYETD RGPLFPTTQD LQGRDTLNDS YHAKVETPWK LLHANSWGC WFSPADFQQM ITTCRDIAPI QMHQKIENIV IKTVSKTGTG ETETTNYNND LTALLQIAQD NSNLLPWAAD N FYIDSVGY ...String: GSGVGHSTGD YNNRTEFIYH GDEVTIICHS TRLVHINMSD REDYIIYETD RGPLFPTTQD LQGRDTLNDS YHAKVETPWK LLHANSWGC WFSPADFQQM ITTCRDIAPI QMHQKIENIV IKTVSKTGTG ETETTNYNND LTALLQIAQD NSNLLPWAAD N FYIDSVGY VPWRACKLPT YCYHVDTWNT IDINQADTPN QWREIKKGIQ WDNIQFTPLE TMINIDLLRT GDAWQSGNYT FH TKPTNLA YHWQSQRHTG SCHPTVAPLV ERGQGTNIQS VNCWQWGDRN NPSSASTRVS NIHIGYSFPE WQIHYSTGGP VIN PGSAFS QAPWGSTTEG TRLTQGASEK AIYDWSHGDD QPGARETWWQ NNQHATGQTD WAPKNAHTSE LNNNVPAATH FWKN SYHNT FSPFTAVDDH GPQYPWGAIW GKYPDTTHKP MMSAHAPFLL HGPPGQLFVK LAPNYTDTLD NGGITHPRIV TYGTF WWSG KLVFKGKLRT PRQWNTYNLP SLDKRETMKN TVPNEVGHFE LPYMPGRCLP NYTL UniProtKB: VP2 |
-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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Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 75.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM / Number images used: 15296 |
Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: RANDOM ASSIGNMENT |