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- EMDB-8748: Cryo-EM reconstruction of the Cafeteria roenbergensis virus capsi... -

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Basic information

Entry
Database: EMDB / ID: 8748
TitleCryo-EM reconstruction of the Cafeteria roenbergensis virus capsid suggests a novel assembly pathway for giant viruses
SampleCafeteria roenbergensis virus BV-PW1
SourceCafeteria roenbergensis virus BV-PW1 / virus
Map dataCryo-EM reconstruction of Cafeteria roenbergensis virus with icosahedral averaging
Methodsingle particle (icosahedral) reconstruction, at 21 Å resolution
AuthorsXiao C / Fischer MG / Bolotaulo DM / Ulloa-Rondeau N / Avila GA / Suttle CA
CitationSci Rep, 2017, 7, 5484-5484

Sci Rep, 2017, 7, 5484-5484 StrPapers
Cryo-EM reconstruction of the Cafeteria roenbergensis virus capsid suggests novel assembly pathway for giant viruses.
Chuan Xiao / Matthias G Fischer / Duer M Bolotaulo / Nancy Ulloa-Rondeau / Gustavo A Avila / Curtis A Suttle

DateDeposition: May 27, 2017 / Header (metadata) release: Jul 19, 2017 / Map release: Aug 2, 2017 / Last update: Aug 2, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.5
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 3.5
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 3.5
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_8748.map.gz (map file in CCP4 format, 549553 KB)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
516 pix
6.16 Å/pix.
= 3176.496 Å
516 pix
6.16 Å/pix.
= 3176.496 Å
516 pix
6.16 Å/pix.
= 3176.496 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 6.156 Å
Density
Contour Level:3.5 (by author), 3.5 (movie #1):
Minimum - Maximum-2.8819191 - 7.53418
Average (Standard dev.)0.42621794 (1.369907)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions516516516
Origin000
Limit515515515
Spacing516516516
CellA=B=C: 3176.496 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z6.1566.1566.156
M x/y/z516516516
origin x/y/z0.0000.0000.000
length x/y/z3176.4963176.4963176.496
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS516516516
D min/max/mean-2.8827.5340.426

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Supplemental data

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Mask #1

Fileemd_8748_msk_1.map ( map file in CCP4 format, 549553 KB )
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms
Data typeImage stored as Reals
Annotation detailsSoft mask for the capsid of the odd map for FSC resolution calculation
Space group number1

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Mask #2

Fileemd_8748_msk_2.map ( map file in CCP4 format, 549553 KB )
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms
Data typeImage stored as Reals
Annotation detailsSoft mask for the capsid of the odd map for FSC resolution calculation
Space group number1

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Mask #2~

Fileemd_8748_msk_2.map
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

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Sample components

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Entire Cafeteria roenbergensis virus BV-PW1

EntireName: Cafeteria roenbergensis virus BV-PW1
Details: The virus was purified following the protocol described in Fischer, M.G., et. al. The virion of Cafeteria roenbergensis virus (CroV) contains a complex suite of proteins for transcription and DNA repair - Virology 466-467, 82-94 (2014).
Number of components: 1

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Component #1: virus, Cafeteria roenbergensis virus BV-PW1

VirusName: Cafeteria roenbergensis virus BV-PW1 / Class: VIRION
Details: The virus was purified following the protocol described in Fischer, M.G., et. al. The virion of Cafeteria roenbergensis virus (CroV) contains a complex suite of proteins for transcription and DNA repair - Virology 466-467, 82-94 (2014).
Empty: No / Enveloped: No / Isolate: SPECIES
SpeciesSpecies: Cafeteria roenbergensis virus BV-PW1 / virus / Strain: BV-PW1
Source (natural)Host Species: Cafeteria roenbergensis
Shell #1Name of element: CroV / Diameter: 3000 Å / T number(triangulation number): 499

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionpH: 7.2
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE

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Electron microscopy imaging

ImagingMicroscope: FEI/PHILIPS CM300FEG/ST
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 25 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: DARK FIELD
Specimen HolderModel: OTHER
CameraDetector: KODAK SO-163 FILM

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Image processing

ProcessingMethod: single particle (icosahedral) reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 2471
3D reconstructionAlgorithm: FOURIER SPACE / Software: Frealign / Resolution: 21 Å / Resolution method: FSC 0.33 CUT-OFF
Details: The two maps were softmasked for only the capsid part.
FSC plot (resolution assessment)

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