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- EMDB-7880: Infectious microvesicles (Class 1 and 3) from poliovirus-infected... -

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Entry
Database: EMDB / ID: EMD-7880
TitleInfectious microvesicles (Class 1 and 3) from poliovirus-infected HeLa cells, displaying clusters of virions and additional inner vesicular structures
Map data
SampleHuman poliovirus 1 Mahoney:
virus
Biological speciesHuman poliovirus 1 Mahoney
Methodelectron tomography / cryo EM
AuthorsYang JE
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical SciencesR01 GM102474 United States
National Institutes of Health/National Institute of General Medical SciencesU24GM116787 United States
CitationJournal: Sci Rep / Year: 2020
Title: Complexity and ultrastructure of infectious extracellular vesicles from cells infected by non-enveloped virus.
Authors: Jie E Yang / Evan D Rossignol / Deborah Chang / Joseph Zaia / Isaac Forrester / Kiran Raja / Holly Winbigler / Daniela Nicastro / William T Jackson / Esther Bullitt /
Abstract: Enteroviruses support cell-to-cell viral transmission prior to their canonical lytic spread of virus. Poliovirus (PV), a prototype for human pathogenic positive-sense RNA enteroviruses, and ...Enteroviruses support cell-to-cell viral transmission prior to their canonical lytic spread of virus. Poliovirus (PV), a prototype for human pathogenic positive-sense RNA enteroviruses, and picornaviruses in general, transport multiple virions en bloc via infectious extracellular vesicles, 100~1000 nm in diameter, secreted from host cells. Using biochemical and biophysical methods we identify multiple components in secreted microvesicles, including mature PV virions; positive-sense genomic and negative-sense replicative, template viral RNA; essential viral replication proteins; and cellular proteins. Using cryo-electron tomography, we visualize the near-native three-dimensional architecture of secreted infectious microvesicles containing both virions and a unique morphological component that we describe as a mat-like structure. While the composition of these mat-like structures is not yet known, based on our biochemical data they are expected to be comprised of unencapsidated RNA and proteins. In addition to infectious microvesicles, CD9-positive exosomes released from PV-infected cells are also infectious and transport virions. Thus, our data show that, prior to cell lysis, non-enveloped viruses are secreted within infectious vesicles that also transport viral unencapsidated RNAs, viral and host proteins. Understanding the structure and function of these infectious particles helps elucidate the mechanism by which extracellular vesicles contribute to the spread of non-enveloped virus infection.
History
DepositionMay 15, 2018-
Header (metadata) releaseJul 25, 2018-
Map releaseMay 15, 2019-
UpdateMay 27, 2020-
Current statusMay 27, 2020Processing site: RCSB / Status: Released

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Structure visualization

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  • Imaged by UCSF Chimera
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Supplemental images

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Map

FileDownload / File: emd_7880.map.gz / Format: CCP4 / Size: 260.9 MB / Type: IMAGE STORED AS SIGNED BYTE
Voxel sizeX=Y=Z: 4.01 Å
Density
Minimum - Maximum-70 - 61
Average (Standard dev.)-1.6020291 (±5.747377)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-2414-886442
Dimensions843753431
Spacing753843431
CellA: 3019.5303 Å / B: 3380.4302 Å / C: 1728.31 Å
α=β=γ: 90.0 °

CCP4 map header:

modeenvelope stored as signed bytes (from -128 lowest to 127 highest)
Å/pix. X/Y/Z4.014.014.01
M x/y/z753843431
origin x/y/z0.0000.0000.000
length x/y/z3019.5303380.4301728.310
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ280280280
MAP C/R/S123
start NC/NR/NS-886-2414442
NC/NR/NS753843431
D min/max/mean-70.00061.000-1.602

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Supplemental data

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Sample components

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Entire Human poliovirus 1 Mahoney

EntireName: Human poliovirus 1 Mahoney / Number of components: 1

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Component #1: virus, Human poliovirus 1 Mahoney

VirusName: Human poliovirus 1 Mahoney / Class: VIRUS-LIKE PARTICLE / Empty: No / Enveloped: No / Isolate: STRAIN
SpeciesSpecies: Human poliovirus 1 Mahoney
Source (natural)Host Species: Homo sapiens (human)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 1.5 mg/mL / Buffer solution: 1% glutaraldehyde in 1x PBS / pH: 7
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Temperature: 283.15 K / Humidity: 100 %

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Electron microscopy imaging

ImagingMicroscope: JEOL 2200FS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 1.02 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: DIRECT ELECTRON DE-20 (5k x 3k)

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Image processing

ProcessingMethod: electron tomography / Number of sections: 62
3D reconstructionSoftware: eTomo

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