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- EMDB-20747: Low pH-Treated Samba Virus -

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Basic information

Entry
Database: EMDB / ID: EMD-20747
TitleLow pH-Treated Samba Virus
Map dataTomographic reconstruction of a pH 2-treated Samba virus particle.
Sample
  • Virus: Samba virus
Biological speciesSamba virus
Methodelectron tomography / cryo EM
AuthorsSchrad JR / Abrahao JS / Cortines 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-
UpdateJun 10, 2020-
Current statusJun 10, 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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Supplemental images

emd_20747.png

Downloads & links

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Map

FileDownload / File: emd_20747.map.gz / Format: CCP4 / Size: 1.5 GB / Type: IMAGE STORED AS SIGNED BYTE
AnnotationTomographic reconstruction of a pH 2-treated Samba virus particle.
Voxel sizeX=Y=Z: 6.87 Å
Density
Minimum - Maximum-128 - 127
Average (Standard dev.)-6.6646166 (±5.1945395)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-341-22840
Dimensions18531709496
Spacing17091853496
CellA: 11740.83 Å / B: 12730.109 Å / C: 3407.52 Å
α=β=γ: 90.0 °

CCP4 map header:

modeenvelope stored as signed bytes (from -128 lowest to 127 highest)
Å/pix. X/Y/Z6.876.86999946033466.87
M x/y/z17091853496
origin x/y/z0.0000.0000.000
length x/y/z11740.83012730.1093407.520
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-228-34140
NC/NR/NS17091853496
D min/max/mean-128.000127.000-6.665

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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 / Details: Low pH-treated Samba virus particles. / 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) / 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 phosphate
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Atmosphere: AIR / Details: Fischione model 1020
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER
DetailsLow pH-treated Samba virus particles ~1x10^9 particles per mL
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 opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 1.4 mm / Nominal defocus min: -0.015 µm / Nominal magnification: 8000
Specialist opticsEnergy filter - Name: In-column Omega Filter / Energy filter - Slit width: 35 eV
Sample stageSpecimen holder model: GATAN 914 HIGH TILT LIQUID NITROGEN CRYO TRANSFER TOMOGRAPHY HOLDER
Cooling holder cryogen: NITROGEN
TemperatureMin: 70.0 K / Max: 70.0 K
Image recordingFilm or detector model: DIRECT ELECTRON DE-20 (5k x 3k) / Detector mode: INTEGRATING / Digitization - Sampling interval: 6.4 µm / Digitization - Frames/image: 1-25 / Average exposure time: 1.5 sec. / Average electron dose: 3.0 e/Å2

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Image processing

Final reconstructionAlgorithm: SIMULTANEOUS ITERATIVE (SIRT) / Software - Name: IMOD (ver. 4.7.5) / Number images used: 41
DetailsDE motion correction software used for image alignment

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