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- EMDB-6310: A Virus that Infects a Hyperthermophile Encapsidates A-Form DNA -

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Basic information

Entry
Database: EMDB / ID: EMD-6310
TitleA Virus that Infects a Hyperthermophile Encapsidates A-Form DNA
Map dataReconstruction of SIRV2
Sample
  • Sample: SIRV2
  • Virus: Sulfolobus islandicus rod-shaped virus 2
Keywordsarchaeal virus / helical symmetry
Function / homologySulfolobus virus, coat protein, C-terminal / Sulfolobus virus coat protein C terminal / helical viral capsid / DNA binding / Major capsid protein
Function and homology information
Biological speciesSulfolobus islandicus rod-shaped virus 2
Methodhelical reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsDiMaio F / Yu X / Rensen E / Krupovic M / Prangishvili D / Egelman E
CitationJournal: Science / Year: 2015
Title: Virology. A virus that infects a hyperthermophile encapsidates A-form DNA.
Authors: Frank DiMaio / Xiong Yu / Elena Rensen / Mart Krupovic / David Prangishvili / Edward H Egelman /
Abstract: Extremophiles, microorganisms thriving in extreme environmental conditions, must have proteins and nucleic acids that are stable at extremes of temperature and pH. The nonenveloped, rod-shaped virus ...Extremophiles, microorganisms thriving in extreme environmental conditions, must have proteins and nucleic acids that are stable at extremes of temperature and pH. The nonenveloped, rod-shaped virus SIRV2 (Sulfolobus islandicus rod-shaped virus 2) infects the hyperthermophilic acidophile Sulfolobus islandicus, which lives at 80°C and pH 3. We have used cryo-electron microscopy to generate a three-dimensional reconstruction of the SIRV2 virion at ~4 angstrom resolution, which revealed a previously unknown form of virion organization. Although almost half of the capsid protein is unstructured in solution, this unstructured region folds in the virion into a single extended α helix that wraps around the DNA. The DNA is entirely in the A-form, which suggests a common mechanism with bacterial spores for protecting DNA in the most adverse environments.
History
DepositionMar 19, 2015-
Header (metadata) releaseApr 8, 2015-
Map releaseJun 3, 2015-
UpdateJun 3, 2015-
Current statusJun 3, 2015Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.14
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.14
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3j9x
  • Surface level: 0.14
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3j9x
  • Surface level: 0.14
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3j9x
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

400_6310.gif

Downloads & links

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Map

FileDownload / File: emd_6310.map.gz / Format: CCP4 / Size: 31.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of SIRV2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 128 pix.
= 134.4 Å		1.05 Å/pix.
x 256 pix.
= 268.8 Å		1.05 Å/pix.
x 256 pix.
= 268.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.14 / Movie #1: 0.14
Minimum - Maximum-0.24791992 - 0.3934437
Average (Standard dev.)0.01061555 (±0.06525622)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-128-128-64
Dimensions256256128
Spacing256256128
CellA: 268.8 Å / B: 268.8 Å / C: 134.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z256256128
origin x/y/z0.0000.0000.000
length x/y/z268.800268.800134.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-128-128-64
NC/NR/NS256256128
D min/max/mean-0.2480.3930.011

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Supplemental data

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Sample components

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Entire : SIRV2

EntireName: SIRV2
Components
  • Sample: SIRV2
  • Virus: Sulfolobus islandicus rod-shaped virus 2

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Supramolecule #1000: SIRV2

SupramoleculeName: SIRV2 / type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: Sulfolobus islandicus rod-shaped virus 2

SupramoleculeName: Sulfolobus islandicus rod-shaped virus 2 / type: virus / ID: 1 / Name.synonym: SIRV2 / NCBI-ID: 157899 / Sci species name: Sulfolobus islandicus rod-shaped virus 2 / Database: NCBI / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No / Syn species name: SIRV2
Host (natural)Organism: Sulfolobus islandicus (archaea) / synonym: ARCHAEA

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 6
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
DateSep 19, 2014
Image recordingCategory: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Number real images: 437 / Average electron dose: 20 e/Å2 / Bits/pixel: 16
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsIHRSR
Final reconstructionApplied symmetry - Helical parameters - Δz: 2.9 Å
Applied symmetry - Helical parameters - Δ&Phi: 24.5 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: OTHER / Software - Name: Spider
CTF correctionDetails: multiply images by CTF, divide reconstruction by sum of CTF**2

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