+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22010 | |||||||||
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Title | The Tusavirus (TuV) capsid structure | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Icosahedral Capsid / Tusavirus / TuV / VIRUS / Protoparvovirus | |||||||||
Function / homology | Function and homology information permeabilization of host organelle membrane involved in viral entry into host cell / symbiont entry into host cell via permeabilization of inner membrane / T=1 icosahedral viral capsid / clathrin-dependent endocytosis of virus by host cell / structural molecule activity / virion attachment to host cell Similarity search - Function | |||||||||
Biological species | Tusavirus 1 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.88 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_22010.map.gz | 227.1 MB | EMDB map data format | |
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Header (meta data) | emd-22010-v30.xml emd-22010.xml | 10.1 KB 10.1 KB | Display Display | EMDB header |
Images | emd_22010.png | 307.6 KB | ||
Filedesc metadata | emd-22010.cif.gz | 5.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22010 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22010 | HTTPS FTP |
-Related structure data
Related structure data | 6x2kMC 6x2iC 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_22010.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.071 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 : Tusavirus 1
Entire | Name: Tusavirus 1 |
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Components |
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-Supramolecule #1: Tusavirus 1
Supramolecule | Name: Tusavirus 1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 1560340 / Sci species name: Tusavirus 1 / 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: Tusavirus 1 |
Molecular weight | Theoretical: 61.204824 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: AGGVGVSTGD FDNTTLWDFH EDGTATITCN STRLVHLTRP DSLDYKIIPT QNNTAVQTVG HMMDDDNHTQ VLTPWSLVDC NAWGVWLSP HDWQHIMNIG EELELLSLEQ EVFNVTLKTA TETGPPESRI TMYNNDLTAV MMITTDTNNQ LPYTPAAIRS E TLGFYPWR ...String: AGGVGVSTGD FDNTTLWDFH EDGTATITCN STRLVHLTRP DSLDYKIIPT QNNTAVQTVG HMMDDDNHTQ VLTPWSLVDC NAWGVWLSP HDWQHIMNIG EELELLSLEQ EVFNVTLKTA TETGPPESRI TMYNNDLTAV MMITTDTNNQ LPYTPAAIRS E TLGFYPWR PTVVPRWRYY FDWDRFLSVT SSSDQSTSII NHSSTQSAIG QFFVIETQLP IALLRTGDSY ATGGYKFDCN KV NLGRHWQ TTRSLGLPPK IEPPTSESAL GTINQNARLA WRWGINDVHE TNVVRPCTAG YNHPEWFYTH TLEGPAIDPA PPT SIPSNW GGGTPPDTRA SSHNQQRITY NYNHGNKDEN LNNFSLNPNN IEGSIINQGN FLSYEGNGQQ INTTAGVAKN GETA TSDPN LVRYMPNTYG VYTAVDHQGP VYPHGQIWDK QIHTDKKPEL HCLAPFTCKN NPPGQMFVRI APNLTDTFNA TPTFS EIIT YADFWWKGTL KMKIKLRPPH QWNIATVLGA AVNIGDAARF VPNRLGQLEF PVINGRIVPS TVY 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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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 75.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER |
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Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: RANDOM ASSIGNMENT |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.88 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM / Number images used: 33191 |