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- EMDB-8599: Samba Virus tomogram -

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Basic information

Entry
Database: EMDB / ID: EMD-8599
TitleSamba Virus tomogram
Map dataSamba Virus particle
Sample
  • Virus: Samba virus
Biological speciesSamba virus
Methodelectron tomography / cryo EM
AuthorsSchrad JR / Young EJ / Abrahao JS / Cortines JR / Parent KN
Funding support United States, 1 items
OrganizationGrant numberCountry
AAASMarion Milligan Mason Award United States
CitationJournal: 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
DepositionFeb 10, 2017-
Header (metadata) releaseFeb 22, 2017-
Map releaseFeb 22, 2017-
UpdateFeb 3, 2021-
Current statusFeb 3, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
  • Download
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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  • Simplified surface model
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8599.png

Downloads & links

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Map

FileDownload / File: emd_8599.map.gz / Format: CCP4 / Size: 279.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSamba Virus particle
Voxel sizeX=Y=Z: 14.7 Å
Density
Minimum - Maximum-587884.1 - 527176.7
Average (Standard dev.)-11709.452 (±16132.14)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions557575229
Spacing575557229
CellA: 8452.5 Å / B: 8187.9 Å / C: 3366.3 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z14.714.714.7
M x/y/z575557229
origin x/y/z0.0000.0000.000
length x/y/z8452.5008187.9003366.300
α/β/γ90.00090.00090.000
start NX/NY/NZ-210-210-210
NX/NY/NZ420420420
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS575557229
D min/max/mean-587884.125527176.688-11709.452

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Supplemental data

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Additional map: Samba Virus particle, inverted map

Fileemd_8599_additional.map
AnnotationSamba Virus particle, inverted map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Samba Virus particle, inverted map

Fileemd_8599_additional_1.map
AnnotationSamba Virus particle, inverted map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Samba virus

EntireName: Samba virus
Components
  • Virus: Samba virus

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Supramolecule #1: Samba virus

SupramoleculeName: 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
Host (natural)Organism: Acanthamoeba castellanii (eukaryote)
Virus shellShell ID: 1 / Diameter: 8400.0 Å

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4 / Component - Concentration: 20.0 mM / Component - Name: sodium phosphate
GridModel: Quantifoil 3.5/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: Aldrich / Diameter: 10 nm

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Electron microscopy

MicroscopeJEOL 2200FS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 25.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 1.4 mm / Nominal magnification: 4000
Specialist opticsEnergy filter - Name: In-column Omega Filter
Sample stageSpecimen holder model: GATAN 914 HIGH TILT LIQUID NITROGEN CRYO TRANSFER TOMOGRAPHY HOLDER
Cooling holder cryogen: NITROGEN
TemperatureMin: 83.0 K / Max: 83.0 K
Image recordingFilm 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.

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Image processing

Final reconstructionAlgorithm: SIMULTANEOUS ITERATIVE (SIRT) / Software - Name: IMOD (ver. 4.7.15) / Number images used: 67
DetailsThe selected images were motion-corrected and corrected for the gain and dark references prior to performance of the tomographic reconstructions.

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