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- EMDB-2234: Electron cryo-microscopy of a head-tailed virus infecting extreme... -

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Basic information

Entry
Database: EMDB / ID: EMD-2234
TitleElectron cryo-microscopy of a head-tailed virus infecting extremely halophilic archaea
Map dataReconstruction of archaeal virus HVTV-1
Sample
  • Sample: archaeal virus HVTV-1
  • Virus: HVTV-1
KeywordsIcosahedral capsid
Biological speciesHVTV-1
Methodsingle particle reconstruction / cryo EM / Resolution: 10.5 Å
AuthorsPietila MK / Laurinmaki P / Russell DA / Ko CC / Jacobs-Sera D / Butcher SJ / Bamford DH / Hendrix RW
CitationJournal: J Virol / Year: 2013
Title: Insights into head-tailed viruses infecting extremely halophilic archaea.
Authors: Maija K Pietilä / Pasi Laurinmäki / Daniel A Russell / Ching-Chung Ko / Deborah Jacobs-Sera / Sarah J Butcher / Dennis H Bamford / Roger W Hendrix /
Abstract: Extremophilic archaea, both hyperthermophiles and halophiles, dominate in habitats where rather harsh conditions are encountered. Like all other organisms, archaeal cells are susceptible to viral ...Extremophilic archaea, both hyperthermophiles and halophiles, dominate in habitats where rather harsh conditions are encountered. Like all other organisms, archaeal cells are susceptible to viral infections, and to date, about 100 archaeal viruses have been described. Among them, there are extraordinary virion morphologies as well as the common head-tailed viruses. Although approximately half of the isolated archaeal viruses belong to the latter group, no three-dimensional virion structures of these head-tailed viruses are available. Thus, rigorous comparisons with bacteriophages are not yet warranted. In the present study, we determined the genome sequences of two of such viruses of halophiles and solved their capsid structures by cryo-electron microscopy and three-dimensional image reconstruction. We show that these viruses are inactivated, yet remain intact, at low salinity and that their infectivity is regained when high salinity is restored. This enabled us to determine their three-dimensional capsid structures at low salinity to a ∼10-Å resolution. The genetic and structural data showed that both viruses belong to the same T-number class, but one of them has enlarged its capsid to accommodate a larger genome than typically associated with a T=7 capsid by inserting an additional protein into the capsid lattice.
History
DepositionNov 20, 2012-
Header (metadata) releaseNov 28, 2012-
Map releaseJan 16, 2013-
UpdateMar 6, 2013-
Current statusMar 6, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: -400
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: -400
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_2234.tif

Downloads & links

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Map

FileDownload / File: emd_2234.map.gz / Format: CCP4 / Size: 589.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of archaeal virus HVTV-1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.26 Å/pix.
x 541 pix.
= 1222.66 Å		2.26 Å/pix.
x 541 pix.
= 1222.66 Å		2.26 Å/pix.
x 541 pix.
= 1222.66 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.26 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: -500.0 / Movie #1: -400
Minimum - Maximum-1731.0 - 1166.0
Average (Standard dev.)-770.234497069999975 (±234.180633540000002)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions541541541
Spacing541541541
CellA=B=C: 1222.66 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.262.262.26
M x/y/z541541541
origin x/y/z0.0000.0000.000
length x/y/z1222.6601222.6601222.660
α/β/γ90.00090.00090.000
start NX/NY/NZ-36-30-80
NX/NY/NZ7361161
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS541541541
D min/max/mean-1731.0001166.000-770.234

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Supplemental data

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Sample components

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Entire : archaeal virus HVTV-1

EntireName: archaeal virus HVTV-1
Components
  • Sample: archaeal virus HVTV-1
  • Virus: HVTV-1

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Supramolecule #1000: archaeal virus HVTV-1

SupramoleculeName: archaeal virus HVTV-1 / type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: HVTV-1

SupramoleculeName: HVTV-1 / type: virus / ID: 1 / Sci species name: HVTV-1 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Haloarcula vallismortis (Halophile) / synonym: ARCHAEA
Virus shellShell ID: 1 / Diameter: 955 Å / T number (triangulation number): 13

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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 / Details: 20mM Tris-HCl
GridDetails: Quantifoil holey carbon film on 300 mesh copper grid.
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeFEI TECNAI F20
DateOct 8, 2009
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Bits/pixel: 12
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 62000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 2.9 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 62000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 10.5 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: AUTO3DEM / Number images used: 3530

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