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- EMDB-2101: Electron tomography of forming Hepatitis C virus-like particles i... -

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Basic information

Entry
Database: EMDB / ID: EMD-2101
TitleElectron tomography of forming Hepatitis C virus-like particles in insect cells.
Map dataTomographic reconstruction of an insect cell Sf9 producing Hepatitis C virus-like particles.
Sample
  • Sample: Tomographic reconstruction of an insect cell Sf9 producing Hepatitis C virus-like particles
  • Organelle or cellular component: Hepatitis C virus-like particles
KeywordsHepatitis C virus / Hepatitis C virus-like particles / virus morphogenesis / budding
Biological speciesHepatitis C Virus-like particles
Methodelectron tomography / negative staining
AuthorsBadia-Martinez D / Peralta B / Andres G / Guerra M / Gil-Carton D / Abrescia NG
CitationJournal: Virology / Year: 2012
Title: Three-dimensional visualization of forming Hepatitis C virus-like particles by electron-tomography.
Authors: Daniel Badia-Martinez / Bibiana Peralta / German Andrés / Milagros Guerra / David Gil-Carton / Nicola G A Abrescia /
Abstract: Hepatitis C virus infects almost 170 million people per year but its assembly pathway, architecture and the structures of its envelope proteins are poorly understood. Using electron tomography of ...Hepatitis C virus infects almost 170 million people per year but its assembly pathway, architecture and the structures of its envelope proteins are poorly understood. Using electron tomography of plastic-embedded sections of insect cells, we have visualized the morphogenesis of recombinant Hepatitis C virus-like particles. Our data provide a three-dimensional sketch of viral assembly at the endoplasmic reticulum showing different budding stages and contiguity of buds. This latter phenomenon could play an important role during the assembly of wt-HCV and explain the size-heterogeneity of its particles.
History
DepositionMay 16, 2012-
Header (metadata) releaseSep 5, 2012-
Map releaseSep 5, 2012-
UpdateSep 5, 2012-
Current statusSep 5, 2012Processing site: PDBe / Status: Released

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Structure visualization

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  • Imaged by UCSF Chimera
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  • Imaged by UCSF Chimera
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Structure viewerEM map:
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Supplemental images

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Map

FileDownload / File: emd_2101.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTomographic reconstruction of an insect cell Sf9 producing Hepatitis C virus-like particles.
Voxel sizeX=Y=Z: 9.46 Å
Density
Minimum - Maximum0.0 - 180.934158330000002
Average (Standard dev.)15.30517101 (±4.21060133)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions20482048126
Spacing20482048126
CellA: 19374.08 Å / B: 19374.08 Å / C: 1191.96 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z9.469.469.46
M x/y/z20482048126
origin x/y/z0.0000.0000.000
length x/y/z19374.08019374.0801191.960
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ128128168
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS20482048126
D min/max/mean0.000180.93415.305

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Supplemental data

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Sample components

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Entire : Tomographic reconstruction of an insect cell Sf9 producing Hepati...

EntireName: Tomographic reconstruction of an insect cell Sf9 producing Hepatitis C virus-like particles
Components
  • Sample: Tomographic reconstruction of an insect cell Sf9 producing Hepatitis C virus-like particles
  • Organelle or cellular component: Hepatitis C virus-like particles

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Supramolecule #1000: Tomographic reconstruction of an insect cell Sf9 producing Hepati...

SupramoleculeName: Tomographic reconstruction of an insect cell Sf9 producing Hepatitis C virus-like particles
type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: Hepatitis C virus-like particles

SupramoleculeName: Hepatitis C virus-like particles / type: organelle_or_cellular_component / ID: 1 / Name.synonym: HCV-LP / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Hepatitis C Virus-like particles / Cell: Sf9 insect cells / Location in cell: Endoplasmic reticulum

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Experimental details

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Structure determination

Methodnegative staining
Processingelectron tomography

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Sample preparation

StainingType: NEGATIVE
Details: cells were fixed with 2% glutaraldehyde in PBS (pH 7.4), stained with 1% OsO4 and processed for conventional Epon resin embedding
GridDetails: 200 mesh copper EM grids counterstained with uranyl acetate and lead citrate
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeJEOL 2200FS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: -7.0 µm / Nominal defocus min: -5.0 µm / Nominal magnification: 25000
Specialist opticsEnergy filter - Name: omega
Sample stageSpecimen holder model: JEOL / Tilt series - Axis1 - Min angle: -65 ° / Tilt series - Axis1 - Max angle: 65 ° / Tilt series - Axis1 - Angle increment: 1.5 °
TemperatureMin: 292 K / Max: 294 K / Average: 293 K
DateNov 11, 2011
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Number real images: 126 / Bits/pixel: 32

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Image processing

Final reconstructionAlgorithm: OTHER / Software - Name: IMOD, TOMO3D / Number images used: 126

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