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- EMDB-22008: The Cutavirus (CuV) capsid structure -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-22008
TitleThe Cutavirus (CuV) capsid structure
Map data
Sample
  • Virus: Cutavirus
    • Protein or peptide: VP2
KeywordsIcosahedral Capsid / Cutavirus / CuV / 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
Parvovirus coat protein VP2 / Parvovirus coat protein VP1/VP2 / Parvovirus coat protein VP2 / Capsid/spike protein, ssDNA virus
Similarity search - Domain/homology
Biological speciesCutavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.87 Å
AuthorsMietzsch M / Agbandje-McKenna M
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM082946 United States
CitationJournal: 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
DepositionMay 20, 2020-
Header (metadata) releaseJul 1, 2020-
Map releaseJul 1, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6x2i
  • Surface level: 3
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22008.png

Downloads & links

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Map

FileDownload / File: emd_22008.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.057 Å
Density
Contour LevelBy AUTHOR: 1.5 / Movie #1: 3
Minimum - Maximum-9.331505 - 16.658660000000001
Average (Standard dev.)-0.000000003601706 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-210-210-210
Dimensions420420420
Spacing420420420
CellA=B=C: 443.94 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0571.0571.057
M x/y/z420420420
origin x/y/z0.0000.0000.000
length x/y/z443.940443.940443.940
α/β/γ90.00090.00090.000
start NX/NY/NZ-210-210-210
NX/NY/NZ420420420
MAP C/R/S213
start NC/NR/NS-210-210-210
NC/NR/NS420420420
D min/max/mean-9.33216.659-0.000

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Supplemental data

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Sample components

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Entire : Cutavirus

EntireName: Cutavirus
Components
  • Virus: Cutavirus
    • Protein or peptide: VP2

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Supramolecule #1: Cutavirus

SupramoleculeName: 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

MacromoleculeName: VP2 / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO
Source (natural)Organism: Cutavirus
Molecular weightTheoretical: 61.252547 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: 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

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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

BufferpH: 7.4
GridDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm 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

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Image processing

Startup modelType of model: OTHER
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM / Number images used: 15296

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