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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: EMD-8748
TitleCryo-EM reconstruction of the Cafeteria roenbergensis virus capsid suggests a novel assembly pathway for giant viruses
Map dataCryo-EM reconstruction of Cafeteria roenbergensis virus with icosahedral averaging
Sample
  • Virus: Cafeteria roenbergensis virus BV-PW1
Biological speciesCafeteria roenbergensis virus BV-PW1
Methodsingle particle reconstruction / cryo EM / Resolution: 21.0 Å
AuthorsXiao C / Fischer MG / Bolotaulo DM / Ulloa-Rondeau N / Avila GA / Suttle CA
CitationJournal: Sci Rep / Year: 2017
Title: Cryo-EM reconstruction of the Cafeteria roenbergensis virus capsid suggests novel assembly pathway for giant viruses.
Authors: Chuan Xiao / Matthias G Fischer / Duer M Bolotaulo / Nancy Ulloa-Rondeau / Gustavo A Avila / Curtis A Suttle /
Abstract: Whereas the protein composition and overall shape of several giant virus capsids have been described, the mechanism by which these large capsids assemble remains enigmatic. Here, we present a ...Whereas the protein composition and overall shape of several giant virus capsids have been described, the mechanism by which these large capsids assemble remains enigmatic. Here, we present a reconstruction of the capsid of Cafeteria roenbergensis virus (CroV), one of the largest viruses analyzed by cryo-electron microscopy (cryo-EM) to date. The CroV capsid has a diameter of 3,000 Å and a Triangulation number of 499. Unlike related mimiviruses, the CroV capsid is not decorated with glycosylated surface fibers, but features 30 Å-long surface protrusions that are formed by loops of the major capsid protein. Based on the orientation of capsomers in the cryo-EM reconstruction, we propose that the capsids of CroV and related giant viruses are assembled by a newly conceived assembly pathway that initiates at a five-fold vertex and continuously proceeds outwards in a spiraling fashion.
History
DepositionMay 27, 2017-
Header (metadata) releaseJul 19, 2017-
Map releaseAug 2, 2017-
UpdateJul 18, 2018-
Current statusJul 18, 2018Processing site: RCSB / Status: Released

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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
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  • Surface view colored by radius
  • Surface level: 3.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8748.png

Downloads & links

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Map

FileDownload / File: emd_8748.map.gz / Format: CCP4 / Size: 524.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM reconstruction of Cafeteria roenbergensis virus with icosahedral averaging
Voxel sizeX=Y=Z: 6.156 Å
Density
Contour LevelBy AUTHOR: 3.5 / Movie #1: 3.5
Minimum - Maximum-2.8819191 - 7.53418
Average (Standard dev.)0.42621794 (±1.369907)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions516516516
Spacing516516516
CellA=B=C: 3176.496 Å
α=β=γ: 90.0 °

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-152-37
NX/NY/NZ998271
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
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Mask #2

Fileemd_8748_msk_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Even map without soft masking of the reconstruction...

Fileemd_8748_half_map_1.map
AnnotationEven map without soft masking of the reconstruction of Cafeteria roenbergensis virus with icosahedral averaging
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Odd map without soft masking of the reconstruction...

Fileemd_8748_half_map_2.map
AnnotationOdd map without soft masking of the reconstruction of Cafeteria roenbergensis virus with icosahedral averaging
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cafeteria roenbergensis virus BV-PW1

EntireName: Cafeteria roenbergensis virus BV-PW1
Components
  • Virus: Cafeteria roenbergensis virus BV-PW1

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Supramolecule #1: Cafeteria roenbergensis virus BV-PW1

SupramoleculeName: Cafeteria roenbergensis virus BV-PW1 / type: virus / ID: 1 / Parent: 0
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 ...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).
NCBI-ID: 693272 / Sci species name: Cafeteria roenbergensis virus BV-PW1 / Sci species strain: BV-PW1 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Cafeteria roenbergensis (eukaryote)
Virus shellShell ID: 1 / Name: CroV / Diameter: 3000.0 Å / T number (triangulation number): 499

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.2
GridModel: Quantifoil S7/2 / Material: COPPER
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeFEI/PHILIPS CM300FEG/ST
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: KODAK SO-163 FILM / Average electron dose: 25.0 e/Å2

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Image processing

Particle selectionNumber selected: 6698
CTF correctionSoftware - Name: FREALIGN (ver. 8.10)
Startup modelType of model: OTHER
Details: Used EMAN2 and PFT to generate the initial model, a smooth icosahedron
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: FREALIGN (ver. 8.10)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: FREALIGN (ver. 8.10)
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 21.0 Å / Resolution method: FSC 0.33 CUT-OFF / Software - Name: FREALIGN (ver. 8.10)
Details: The two maps were softmasked for only the capsid part.
Number images used: 2471
FSC plot (resolution estimation)

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