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- EMDB-7878: Noodle-like structure in infectious microvesicles (Class 3) from ... -

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Basic information

Entry
Database: EMDB / ID: EMD-7878
TitleNoodle-like structure in infectious microvesicles (Class 3) from poliovirus-infected HeLa cells
Map data
SampleHuman poliovirus 1 Mahoney:
virus
SourceHuman poliovirus 1 Mahoney
Methodelectron tomography / cryo EM
AuthorsYang JE
CitationJournal: To Be Published
Title: Picornavirus PACKETs accelerate viral RNA replication
Authors: Yang JE / Rossignol ED / Chang D / Zaia J / Forrester I / Nicastro D / Jackson W / Bullitt E
DateDeposition: May 15, 2018 / Header (metadata) release: Jul 25, 2018 / Map release: May 15, 2019 / Update: May 15, 2019

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Structure visualization

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  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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Supplemental images

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Map

FileDownload / File: emd_7878.map.gz / Format: CCP4 / Size: 29.8 MB / Type: IMAGE STORED AS SIGNED BYTE
Voxel sizeX=Y=Z: 8.2 Å
Density
Minimum - Maximum-111.0 - 115.0
Average (Standard dev.)11.651899999999999 (±6.9279456)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-1698-1019227
Dimensions291311345
Spacing311291345
CellA: 2550.2 Å / B: 2386.2 Å / C: 2829.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeenvelope stored as signed bytes (from -128 lowest to 127 highest)
Å/pix. X/Y/Z8.28.28.2
M x/y/z311291345
origin x/y/z0.0000.0000.000
length x/y/z2550.2002386.2002829.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ208208208
MAP C/R/S123
start NC/NR/NS-1019-1698227
NC/NR/NS311291345
D min/max/mean-111.000115.00011.652

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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
Details: virion-containing microvesicles collected from supernatant of poliovirus-infected cells at 8 hours post-infection
Number of components: 1

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Component #1: virus, Human poliovirus 1 Mahoney

VirusName: Human poliovirus 1 Mahoney / Class: VIRUS-LIKE PARTICLE
Details: virion-containing microvesicles collected from supernatant of poliovirus-infected cells at 8 hours post-infection
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
Support filmThe grid was coated with an extra layer of carbon (holes not covered) to provide extra support.
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Temperature: 283.15 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 160 kV / Electron dose: 4.8 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: TVIPS TEMCAM-F416 (4k x 4k)

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Image processing

ProcessingMethod: electron tomography / Number of sections: 47
3D reconstructionAlgorithm: BACK PROJECTION / Software: eTomo

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