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- EMDB-1679: Characterization of the extremophilic, archaeal virus STIV2 -

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Basic information

Entry
Database: EMDB / ID: EMD-1679
TitleCharacterization of the extremophilic, archaeal virus STIV2
Map dataThis is a 20 A resolution cryo-EM reconstruction of the archaeal virus STIV2
Sample
  • Sample: STIV2 virus
  • Virus: Sulfolobus turreted icosahedral virus 2
KeywordsArchaeal / virus / icosahedral / extremophilic
Biological speciesSulfolobus turreted icosahedral virus 2
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 20.0 Å
AuthorsHapponen LJ / Redder P / Peng X / Reigstad LJ / Prangishvili D / Butcher SJ
CitationJournal: J Virol / Year: 2010
Title: Familial relationships in hyperthermo- and acidophilic archaeal viruses.
Authors: Lotta Johanna Happonen / Peter Redder / Xu Peng / Laila Johanne Reigstad / David Prangishvili / Sarah Jane Butcher /
Abstract: Archaea often live in extreme, harsh environments such as acidic hot springs and hypersaline waters. To date, only two icosahedrally symmetric, membrane-containing archaeal viruses, SH1 and ...Archaea often live in extreme, harsh environments such as acidic hot springs and hypersaline waters. To date, only two icosahedrally symmetric, membrane-containing archaeal viruses, SH1 and Sulfolobus turreted icosahedral virus (STIV), have been described in detail. We report the sequence and three-dimensional structure of a third such virus isolated from a hyperthermoacidophilic crenarchaeon, Sulfolobus strain G4ST-2. Characterization of this new isolate revealed it to be similar to STIV on the levels of genome and structural organization. The genome organization indicates that these two viruses have diverged from a common ancestor. Interestingly, the prominent surface turrets of the two viruses are strikingly different. By sequencing and mass spectrometry, we mapped several large insertions and deletions in the known structural proteins that could account for these differences and showed that both viruses can infect the same host. A combination of genomic and proteomic analyses revealed important new insights into the structural organization of these viruses and added to our limited knowledge of archaeal virus life cycles and host-cell interactions.
History
DepositionJan 12, 2010-
Header (metadata) releaseMar 10, 2010-
Map releaseMar 11, 2010-
UpdateSep 9, 2011-
Current statusSep 9, 2011Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 960
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 960
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1679.tif

Downloads & links

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Map

FileDownload / File: emd_1679.map.gz / Format: CCP4 / Size: 130.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a 20 A resolution cryo-EM reconstruction of the archaeal virus STIV2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.42 Å/pix.
x 327 pix.
= 327.08 Å		4.42 Å/pix.
x 327 pix.
= 327.08 Å		4.42 Å/pix.
x 327 pix.
= 327.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.42 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 960.0 / Movie #1: 960
Minimum - Maximum-2959.329999999999927 - 4678.529999999999745
Average (Standard dev.)0.000000058474 (±480.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions327327327
Spacing327327327
CellA=B=C: 327.08 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.424.424.42
M x/y/z747474
origin x/y/z0.0000.0000.000
length x/y/z327.080327.080327.080
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ121121121
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS327327327
D min/max/mean-2959.3294678.5280.000

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Supplemental data

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Sample components

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Entire : STIV2 virus

EntireName: STIV2 virus
Components
  • Sample: STIV2 virus
  • Virus: Sulfolobus turreted icosahedral virus 2

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Supramolecule #1000: STIV2 virus

SupramoleculeName: STIV2 virus / type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: Sulfolobus turreted icosahedral virus 2

SupramoleculeName: Sulfolobus turreted icosahedral virus 2 / type: virus / ID: 1 / Name.synonym: STIV2 / NCBI-ID: 754004 / Sci species name: Sulfolobus turreted icosahedral virus 2 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: STIV2
Host (natural)Organism: Sulfolobus islandicus (archaea) / synonym: ARCHAEA
Virus shellShell ID: 1 / Diameter: 710 Å / T number (triangulation number): 31

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 3.5 / Details: 50 mM sodium citrate, pH 3.5
StainingType: NEGATIVE
Details: Vitrified. Grids were blotted for roughly one second before being plunged into liquid ethane.
GridDetails: Quantifoil-grids
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: Guillotine
Method: A small vial of ethane is placed inside a larger liquid nitrogen reservoir. The grid holding 3 microliters of the sample is held in place at the bottom of a plunger by the means of fine ...Method: A small vial of ethane is placed inside a larger liquid nitrogen reservoir. The grid holding 3 microliters of the sample is held in place at the bottom of a plunger by the means of fine tweezers. When the liquid ethane is ready, a piece of filter paper is then pressed against the sample to blot off excess buffer, sufficient to leave a thin layer on the grid. The filter paper is removed, and the plunger is allowed to drop into the liquid ethane. Once the grid enters the liquid ethane, the sample is rapidly frozen, and the grid is transferred under liquid nitrogen to a storage box immersed in liquid nitrogen for later use in the microscope.

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Electron microscopy

MicroscopeFEI TECNAI F20
DetailsLow dose conditions
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Sampling interval: 4.42 µm / Number real images: 358 / Average electron dose: 18 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 66400 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 5.2 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 68000
Sample stageSpecimen holder: Side entry liquid nitrogen-cooled side entry holder
Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each micrograph
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: PFT, POR, EM3DR2, P3DR / Number images used: 713

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