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- EMDB-8753: Multi-membrane Structure of the Pandoravirus and Implications to ... -

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Basic information

Entry
Database: EMDB / ID: EMD-8753
TitleMulti-membrane Structure of the Pandoravirus and Implications to Eukaryogenesis
Map dataCryo-ET Tomogram of P. dulcis
Sample
  • Virus: Pandoravirus salinus
Biological speciesPandoravirus salinus
Methodelectron tomography / cryo EM
AuthorsWang KJ / Zhou ZH
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM071940 and Al094386 United States
CitationJournal: To Be Published
Title: In depth examination of the various structures of P. salinus through CryoET reconstructions
Authors: Wang KJ / Zhou ZH
History
DepositionJun 5, 2017-
Header (metadata) releaseJul 19, 2017-
Map releaseJul 19, 2017-
UpdateJan 29, 2020-
Current statusJan 29, 2020Processing 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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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8753.png

Downloads & links

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Map

FileDownload / File: emd_8753.map.gz / Format: CCP4 / Size: 1.5 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-ET Tomogram of P. dulcis
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
7.07 Å/pix.
x 465 pix.
= 3285.69 Å		7.07 Å/pix.
x 928 pix.
= 6557.248 Å		7.07 Å/pix.
x 928 pix.
= 6557.248 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: 7.066 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-2404.3599 - 1108.582
Average (Standard dev.)7.2172174 (±70.62945)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin00132
Dimensions928928465
Spacing928928465
CellA: 6557.248 Å / B: 6557.248 Å / C: 3285.69 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z7.0667.0667.066
M x/y/z928928465
origin x/y/z0.0000.0000.000
length x/y/z6557.2486557.2483285.690
α/β/γ90.00090.00090.000
start NX/NY/NZ-38-19-20
NX/NY/NZ858082
MAP C/R/S123
start NC/NR/NS00132
NC/NR/NS928928465
D min/max/mean-2404.3601108.5827.217

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Supplemental data

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Sample components

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Entire : Pandoravirus salinus

EntireName: Pandoravirus salinus
Components
  • Virus: Pandoravirus salinus

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Supramolecule #1: Pandoravirus salinus

SupramoleculeName: Pandoravirus salinus / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 1349410 / Sci species name: Pandoravirus salinus / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Acanthamoeba (eukaryote)

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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
Sugar embeddingMaterial: vitreous ice
GridModel: Quantifoil 200 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: NITROGEN / Instrument: FEI VITROBOT MARK IV
High pressure freezingInstrument: OTHER
Details: The value given for _emd_high_pressure_freezing.instrument is Leica EM PACT2. This is not in a list of allowed values set(['LEICA EM PACT2', 'LEICA EM PACT', 'EMS-002 RAPID IMMERSION ...Details: The value given for _emd_high_pressure_freezing.instrument is Leica EM PACT2. This is not in a list of allowed values set(['LEICA EM PACT2', 'LEICA EM PACT', 'EMS-002 RAPID IMMERSION FREEZER', 'OTHER', 'LEICA EM HPM100', 'BAL-TEC HPM 010']) so OTHER is written into the XML file.
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: Nanogold / Diameter: 10 nm

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average electron dose: 100.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionAlgorithm: SIMULTANEOUS ITERATIVE (SIRT) / Software - Name: IMOD (ver. 4.7.15) / Number images used: 64

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