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Yorodumi- EMDB-2101: Electron tomography of forming Hepatitis C virus-like particles i... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2101 | |||||||||
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Title | Electron tomography of forming Hepatitis C virus-like particles in insect cells. | |||||||||
Map data | Tomographic reconstruction of an insect cell Sf9 producing Hepatitis C virus-like particles. | |||||||||
Sample |
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Keywords | Hepatitis C virus / Hepatitis C virus-like particles / virus morphogenesis / budding | |||||||||
Biological species | Hepatitis C Virus-like particles | |||||||||
Method | electron tomography / negative staining | |||||||||
Authors | Badia-Martinez D / Peralta B / Andres G / Guerra M / Gil-Carton D / Abrescia NG | |||||||||
Citation | Journal: 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 |
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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_2101.map.gz | 1.7 GB | EMDB map data format | |
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Header (meta data) | emd-2101-v30.xml emd-2101.xml | 8.6 KB 8.6 KB | Display Display | EMDB header |
Images | EMD-2101.png | 289.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2101 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2101 | HTTPS FTP |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_2101.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Tomographic reconstruction of an insect cell Sf9 producing Hepatitis C virus-like particles. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 9.46 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 : Tomographic reconstruction of an insect cell Sf9 producing Hepati...
Entire | Name: Tomographic reconstruction of an insect cell Sf9 producing Hepatitis C virus-like particles |
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Components |
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-Supramolecule #1000: Tomographic reconstruction of an insect cell Sf9 producing Hepati...
Supramolecule | Name: 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
Supramolecule | Name: Hepatitis C virus-like particles / type: organelle_or_cellular_component / ID: 1 / Name.synonym: HCV-LP / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: Hepatitis C Virus-like particles / Cell: Sf9 insect cells / Location in cell: Endoplasmic reticulum |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | electron tomography |
-Sample preparation
Staining | Type: NEGATIVE Details: cells were fixed with 2% glutaraldehyde in PBS (pH 7.4), stained with 1% OsO4 and processed for conventional Epon resin embedding |
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Grid | Details: 200 mesh copper EM grids counterstained with uranyl acetate and lead citrate |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
-Electron microscopy
Microscope | JEOL 2200FS |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination 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 optics | Energy filter - Name: omega |
Sample stage | Specimen holder model: JEOL / Tilt series - Axis1 - Min angle: -65 ° / Tilt series - Axis1 - Max angle: 65 ° / Tilt series - Axis1 - Angle increment: 1.5 ° |
Temperature | Min: 292 K / Max: 294 K / Average: 293 K |
Date | Nov 11, 2011 |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Number real images: 126 / Bits/pixel: 32 |
-Image processing
Final reconstruction | Algorithm: OTHER / Software - Name: IMOD, TOMO3D / Number images used: 126 |
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