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- EMDB-20745: Low pH and high temperature-treated Samba virus particles -

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Basic information

Entry
Database: EMDB / ID: EMD-20745
TitleLow pH and high temperature-treated Samba virus particles
Map dataLow pH and high temperature-treated Samba virus particles
Sample
  • Virus: Samba virus
Biological speciesSamba virus
Methodelectron tomography / cryo EM
AuthorsSchrad JR / Parent KN
Funding support United States, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical SciencesU24GM116789-03 United States
AAAS Marion Mason Milligan Award for Women in the Chemical Sciences United States
National Institutes of Health/National Human Genome Research InstituteGM110185 United States
NVIDIA GPU grant program United States
Burroughs Wellcome Fund Investigators in the Pathogenicity of Disease United States
CitationJournal: Cell / Year: 2020
Title: Structural and Proteomic Characterization of the Initiation of Giant Virus Infection.
Authors: Jason R Schrad / Jônatas S Abrahão / Juliana R Cortines / Kristin N Parent /
Abstract: Since their discovery, giant viruses have expanded our understanding of the principles of virology. Due to their gargantuan size and complexity, little is known about the life cycles of these viruses. ...Since their discovery, giant viruses have expanded our understanding of the principles of virology. Due to their gargantuan size and complexity, little is known about the life cycles of these viruses. To answer outstanding questions regarding giant virus infection mechanisms, we set out to determine biomolecular conditions that promote giant virus genome release. We generated four infection intermediates in Samba virus (Mimivirus genus, lineage A) as visualized by cryoelectron microscopy (cryo-EM), cryoelectron tomography (cryo-ET), and scanning electron microscopy (SEM). Each of these four intermediates reflects similar morphology to a stage that occurs in vivo. We show that these genome release stages are conserved in other mimiviruses. Finally, we identified proteins that are released from Samba and newly discovered Tupanvirus through differential mass spectrometry. Our work revealed the molecular forces that trigger infection are conserved among disparate giant viruses. This study is also the first to identify specific proteins released during the initial stages of giant virus infection.
History
DepositionSep 20, 2019-
Header (metadata) releaseOct 2, 2019-
Map releaseMay 13, 2020-
UpdateMay 13, 2020-
Current statusMay 13, 2020Processing site: RCSB / Status: Released

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Structure visualization

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

emd_20745.png

Downloads & links

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Map

FileDownload / File: emd_20745.map.gz / Format: CCP4 / Size: 1.2 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLow pH and high temperature-treated Samba virus particles
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.24 Å/pix.
x 399 pix.
= 1691.76 Å		4.24 Å/pix.
x 881 pix.
= 3735.44 Å		4.24 Å/pix.
x 954 pix.
= 4044.96 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 4.24 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-12.587518 - 3.9867213
Average (Standard dev.)-0.5359285 (±0.42717564)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-17-115278
Dimensions881954399
Spacing954881399
CellA: 4044.9597 Å / B: 3735.4397 Å / C: 1691.7599 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.244.244.24
M x/y/z954881399
origin x/y/z0.0000.0000.000
length x/y/z4044.9603735.4401691.760
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ240240240
MAP C/R/S123
start NC/NR/NS-115-17278
NC/NR/NS954881399
D min/max/mean-12.5883.987-0.536

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Supplemental data

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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 / Macromolecule list: #1
Details: Low pH and high temperature-treated Samba virus particle.
NCBI-ID: 1461100 / Sci species name: Samba virus / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Acanthamoeba castellanii (eukaryote) / Strain: Neff

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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: 2 / Component - Concentration: 20.0 mM / Component - Formula: NaPO4 / Component - Name: sodium phosphage
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Pretreatment - Type: PLASMA CLEANING / Details: Fischione model 1020
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER
Details~1 x 10^9 particles per mL
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: Aldrich / Diameter: 10 nm

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 70.0 K / Max: 70.0 K
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average exposure time: 5.0 sec. / Average electron dose: 2.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 33000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsMotionCor processing to create final aligned images
Final reconstructionAlgorithm: SIMULTANEOUS ITERATIVE (SIRT) / Software - Name: IMOD (ver. 4.7.5) / Number images used: 51

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