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- EMDB-2279: Electron cryo-microscopy of a head-tailed virus infecting extreme... -

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Basic information

Entry
Database: EMDB / ID: EMD-2279
TitleElectron cryo-microscopy of a head-tailed virus infecting extremely halophilic archaea
Map dataReconstruction of HSTV-1
Sample
  • Sample: archaeal virus HSTV-1
  • Virus: HSTV-1
KeywordsIcosahedral capsid
Biological speciesHSTV-1
Methodsingle particle reconstruction / cryo EM / Resolution: 8.9 Å
AuthorsPietila MK / Laurinmaki P / Russell DA / Ko CC / Jacobs-Sera D / Butcher SJ / Bamford DH / Hendrix RW
CitationJournal: Proc Natl Acad Sci U S A / Year: 2013
Title: Structure of the archaeal head-tailed virus HSTV-1 completes the HK97 fold story.
Authors: Maija K Pietilä / Pasi Laurinmäki / Daniel A Russell / Ching-Chung Ko / Deborah Jacobs-Sera / Roger W Hendrix / Dennis H Bamford / Sarah J Butcher /
Abstract: It has been proposed that viruses can be divided into a small number of structure-based viral lineages. One of these lineages is exemplified by bacterial virus Hong Kong 97 (HK97), which represents ...It has been proposed that viruses can be divided into a small number of structure-based viral lineages. One of these lineages is exemplified by bacterial virus Hong Kong 97 (HK97), which represents the head-tailed dsDNA bacteriophages. Seemingly similar viruses also infect archaea. Here we demonstrate using genomic analysis, electron cryomicroscopy, and image reconstruction that the major coat protein fold of newly isolated archaeal Haloarcula sinaiiensis tailed virus 1 has the canonical coat protein fold of HK97. Although it has been anticipated previously, this is physical evidence that bacterial and archaeal head-tailed viruses share a common architectural principle. The HK97-like fold has previously been recognized also in herpesviruses, and this study expands the HK97-like lineage to viruses from all three domains of life. This is only the second established lineage to include archaeal, bacterial, and eukaryotic viruses. Thus, our findings support the hypothesis that the last common universal ancestor of cellular organisms was infected by a number of different viruses.
History
DepositionJan 11, 2013-
Header (metadata) releaseJan 23, 2013-
Map releaseJul 3, 2013-
UpdateJul 3, 2013-
Current statusJul 3, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1892
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 1892
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_2279.tif

Downloads & links

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Map

FileDownload / File: emd_2279.map.gz / Format: CCP4 / Size: 278 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of HSTV-1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 421 pix.
= 421. Å		1 Å/pix.
x 421 pix.
= 421. Å		1 Å/pix.
x 421 pix.
= 421. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel size
XYZ
EMDB info.111
CCP4 map header111
EM Navigator Movie #12.262.262.26
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1892.0 / Movie #1: 1892
Minimum - Maximum-994.0 - 4081.0
Average (Standard dev.)1194.109375 (±248.554504390000005)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions421421421
Spacing421421421
CellA=B=C: 421.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z111
M x/y/z421421421
origin x/y/z0.0000.0000.000
length x/y/z421.000421.000421.000
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/NS421421421
D min/max/mean-994.0004081.0001194.109

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Supplemental data

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Sample components

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Entire : archaeal virus HSTV-1

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

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Supramolecule #1000: archaeal virus HSTV-1

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

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Supramolecule #1: HSTV-1

SupramoleculeName: HSTV-1 / type: virus / ID: 1 / Sci species name: HSTV-1 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Haloarcula sinaiiensis ATCC 33800 (Halophile) / synonym: ARCHAEA
Virus shellShell ID: 1 / Diameter: 624 Å / T number (triangulation number): 7

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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
DateSep 9, 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: 8.9 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: AUTO3DEM / Number images used: 7115

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