+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8599 | |||||||||
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Title | Samba Virus tomogram | |||||||||
Map data | Samba Virus particle | |||||||||
Sample |
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Biological species | Samba virus | |||||||||
Method | electron tomography / cryo EM | |||||||||
Authors | Schrad JR / Young EJ / Abrahao JS / Cortines JR / Parent KN | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Viruses / Year: 2017 Title: Microscopic Characterization of the Brazilian Giant Samba Virus. Authors: Jason R Schrad / Eric J Young / Jônatas S Abrahão / Juliana R Cortines / Kristin N Parent / Abstract: Prior to the discovery of the mimivirus in 2003, viruses were thought to be physically small and genetically simple. Mimivirus, with its ~750-nm particle size and its ~1.2-Mbp genome, shattered these ...Prior to the discovery of the mimivirus in 2003, viruses were thought to be physically small and genetically simple. Mimivirus, with its ~750-nm particle size and its ~1.2-Mbp genome, shattered these notions and changed what it meant to be a virus. Since this discovery, the isolation and characterization of giant viruses has exploded. One of the more recently discovered giant viruses, Samba virus, is a that was isolated from the Rio Negro in the Brazilian Amazon. Initial characterization of Samba has revealed some structural information, although the preparation techniques used are prone to the generation of structural artifacts. To generate more native-like structural information for Samba, we analyzed the virus through cryo-electron microscopy, cryo-electron tomography, scanning electron microscopy, and fluorescence microscopy. These microscopy techniques demonstrated that Samba particles have a capsid diameter of ~527 nm and a fiber length of ~155 nm, making Samba the largest yet characterized. We also compared Samba to a fiberless mimivirus variant. Samba particles, unlike those of mimivirus, do not appear to be rigid, and quasi-icosahedral, although the two viruses share many common features, including a multi-layered capsid and an asymmetric nucleocapsid, which may be common amongst the . | |||||||||
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_8599.map.gz | 225.8 MB | EMDB map data format | |
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Header (meta data) | emd-8599-v30.xml emd-8599.xml | 12.5 KB 12.5 KB | Display Display | EMDB header |
Images | emd_8599.png | 207.4 KB | ||
Others | emd_8599_additional.map.gz emd_8599_additional_1.map.gz | 225.8 MB 225.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8599 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8599 | HTTPS FTP |
-Validation report
Summary document | emd_8599_validation.pdf.gz | 257.7 KB | Display | EMDB validaton report |
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Full document | emd_8599_full_validation.pdf.gz | 257.3 KB | Display | |
Data in XML | emd_8599_validation.xml.gz | 4.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8599 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8599 | HTTPS FTP |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_8599.map.gz / Format: CCP4 / Size: 279.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Samba Virus particle | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 14.7 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Samba Virus particle, inverted map
File | emd_8599_additional.map | ||||||||||||
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Annotation | Samba Virus particle, inverted map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Samba Virus particle, inverted map
File | emd_8599_additional_1.map | ||||||||||||
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Annotation | Samba Virus particle, inverted map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Samba virus
Entire | Name: Samba virus |
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Components |
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-Supramolecule #1: Samba virus
Supramolecule | Name: Samba virus / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 1461100 / Sci species name: Samba virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
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Host (natural) | Organism: Acanthamoeba castellanii (eukaryote) |
Virus shell | Shell ID: 1 / Diameter: 8400.0 Å |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | electron tomography |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 / Component - Concentration: 20.0 mM / Component - Name: sodium phosphate |
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Grid | Model: Quantifoil 3.5/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING |
Vitrification | Cryogen name: ETHANE / Instrument: HOMEMADE PLUNGER |
Sectioning | Other: NO SECTIONING |
Fiducial marker | Manufacturer: Aldrich / Diameter: 10 nm |
-Electron microscopy
Microscope | JEOL 2200FS |
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Temperature | Min: 83.0 K / Max: 83.0 K |
Specialist optics | Energy filter - Name: In-column Omega Filter |
Image recording | Film or detector model: DIRECT ELECTRON DE-20 (5k x 3k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 5120 pixel / Digitization - Dimensions - Height: 3840 pixel / Digitization - Sampling interval: 6.4 µm / Digitization - Frames/image: 1-45 / Number grids imaged: 17 / Average exposure time: 3.0 sec. / Average electron dose: 1.1 e/Å2 Details: 63 tilt series were collected. From these, 20 complete tomograms were produced, capturing 34 particles. |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Calibrated defocus max: 25.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 1.4 mm / Nominal magnification: 4000 |
Sample stage | Specimen holder model: GATAN 914 HIGH TILT LIQUID NITROGEN CRYO TRANSFER TOMOGRAPHY HOLDER Cooling holder cryogen: NITROGEN |
-Image processing
Details | The selected images were motion-corrected and corrected for the gain and dark references prior to performance of the tomographic reconstructions. |
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Final reconstruction | Algorithm: SIMULTANEOUS ITERATIVE (SIRT) / Software - Name: IMOD (ver. 4.7.15) / Number images used: 67 |