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- EMDB-2061: Icosahedral reconstruction of Salisaeta icosahedral phage 1 (SSIP-1) -

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Basic information

Entry
Database: EMDB / ID: EMD-2061
TitleIcosahedral reconstruction of Salisaeta icosahedral phage 1 (SSIP-1)
Map dataIcosahedral reconstruction of phage SSIP-1
Sample
  • Sample: Salisaeta icosahedral phage 1 (SSIP1) virion
  • Virus: Salisaeta icosahedral phage 1 (virus)
KeywordsSalisaeta icosahedral phage 1 / SSIP-1 / SSIP1 / halophilic / phage / bacteriophage / virus
Biological speciesSalisaeta icosahedral phage 1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 12.5 Å
AuthorsAalto AP / Bitto D / Ravantti JJ / Bamford DH / Huiskonen JT / Oksanen HM
CitationJournal: Proc Natl Acad Sci U S A / Year: 2012
Title: Snapshot of virus evolution in hypersaline environments from the characterization of a membrane-containing Salisaeta icosahedral phage 1.
Authors: Antti P Aalto / David Bitto / Janne J Ravantti / Dennis H Bamford / Juha T Huiskonen / Hanna M Oksanen /
Abstract: The multitude of archaea and bacteria inhabiting extreme environments has only become evident during the last decades. As viruses apply a significant evolutionary force to their hosts, there is an ...The multitude of archaea and bacteria inhabiting extreme environments has only become evident during the last decades. As viruses apply a significant evolutionary force to their hosts, there is an inherent value in learning about viruses infecting these extremophiles. In this study, we have focused on one such unique virus-host pair isolated from a hypersaline environment: an icosahedral, membrane-containing double-stranded DNA virus--Salisaeta icosahedral phage 1 (SSIP-1) and its halophilic host bacterium Salisaeta sp. SP9-1 closely related to Salisaeta longa. The architectural principles, virion composition, and the proposed functions associated with some of the ORFs of the virus are surprisingly similar to those found in viruses belonging to the PRD1-adenovirus lineage. The virion structure, determined by electron cryomicroscopy, reveals that the bulk of the outer protein capsid is composed of upright standing pseudohexameric capsomers organized on a T = 49 icosahedral lattice. Our results give a comprehensive description of a halophilic virus-host system and shed light on the relatedness of viruses based on their virion architecture.
History
DepositionMar 27, 2012-
Header (metadata) releaseMar 30, 2012-
Map releaseApr 20, 2012-
UpdateOct 31, 2012-
Current statusOct 31, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 2
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_2061.png

Downloads & links

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Map

FileDownload / File: emd_2061.map.gz / Format: CCP4 / Size: 1.4 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIcosahedral reconstruction of phage SSIP-1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2 Å/pix.
x 720 pix.
= 1440. Å		2 Å/pix.
x 720 pix.
= 1440. Å		2 Å/pix.
x 720 pix.
= 1440. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0 / Movie #1: 2
Minimum - Maximum-2.73149323 - 6.07137918
Average (Standard dev.)0.2399127 (±0.88735288)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-360-360-360
Dimensions720720720
Spacing720720720
CellA=B=C: 1440.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z222
M x/y/z720720720
origin x/y/z0.0000.0000.000
length x/y/z1440.0001440.0001440.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS-360-360-360
NC/NR/NS720720720
D min/max/mean-2.7316.0710.240

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Supplemental data

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Sample components

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Entire : Salisaeta icosahedral phage 1 (SSIP1) virion

EntireName: Salisaeta icosahedral phage 1 (SSIP1) virion
Components
  • Sample: Salisaeta icosahedral phage 1 (SSIP1) virion
  • Virus: Salisaeta icosahedral phage 1 (virus)

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Supramolecule #1000: Salisaeta icosahedral phage 1 (SSIP1) virion

SupramoleculeName: Salisaeta icosahedral phage 1 (SSIP1) virion / type: sample / ID: 1000 / Oligomeric state: Whole virion / Number unique components: 1

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Supramolecule #1: Salisaeta icosahedral phage 1

SupramoleculeName: Salisaeta icosahedral phage 1 / type: virus / ID: 1 / Name.synonym: SSIP1 / NCBI-ID: 1183239 / Sci species name: Salisaeta icosahedral phage 1 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: No / Syn species name: SSIP1
Host (natural)Organism: Salisaeta sp. SP9-1 (bacteria) / synonym: BACTERIA(EUBACTERIA)
Virus shellShell ID: 1 / Name: Capsid / Diameter: 1000 Å / T number (triangulation number): 49

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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

BufferDetails: 9% salt water (SW) see http://www.haloarchaea.com/resources/halohandbook/Halohandbook_2008_v7.pdf
GridDetails: 200 mesh molybdenum grid with holey carbon, glow discharged
VitrificationCryogen name: HELIUM / Chamber humidity: 80 % / Chamber temperature: 110 K / Instrument: GATAN CRYOPLUNGE 3 / Method: Blot for 4 seconds from opposite side

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Electron microscopy

MicroscopeFEI POLARA 300
TemperatureAverage: 81 K
DateFeb 26, 2011
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 842 / Average electron dose: 20 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 75000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 59000
Sample stageSpecimen holder: liquid nitrogen temperature / Specimen holder model: OTHER
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

DetailsThe particles were manually picked in EMAN2. Initial model was calculated in IMAGIC5. Contrast transfer function correction and icosahedral reconstruction was carried out in EMAN. The final map was low pass filtered to 11 A.
CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 12.5 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN2 / Number images used: 2747

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