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- EMDB-20618: Sulfolobus Turreted Icosahedral Virus with Petals -

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Basic information

Entry
Database: EMDB / ID: EMD-20618
TitleSulfolobus Turreted Icosahedral Virus with Petals
Map dataSulfolbus Turreted Icosahedral Virus with Petals at 27 Angstroms Resolution.
Sample
  • Virus: Sulfolobus turreted icosahedral virus 1
Biological speciesSulfolobus turreted icosahedral virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 27.0 Å
AuthorsTang L / Rice G / Young M / Johnson JE
Funding support United States, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB 013222156 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2004
Title: The structure of a thermophilic archaeal virus shows a double-stranded DNA viral capsid type that spans all domains of life.
Authors: George Rice / Liang Tang / Kenneth Stedman / Francisco Roberto / Josh Spuhler / Eric Gillitzer / John E Johnson / Trevor Douglas / Mark Young /
Abstract: Of the three domains of life (Eukarya, Bacteria, and Archaea), the least understood is Archaea and its associated viruses. Many Archaea are extremophiles, with species that are capable of growth at ...Of the three domains of life (Eukarya, Bacteria, and Archaea), the least understood is Archaea and its associated viruses. Many Archaea are extremophiles, with species that are capable of growth at some of the highest temperatures and extremes of pH of all known organisms. Phylogenetic rRNA-encoding DNA analysis places many of the hyperthermophilic Archaea (species with an optimum growth > or = 80 degrees C) at the base of the universal tree of life, suggesting that thermophiles were among the first forms of life on earth. Very few viruses have been identified from Archaea as compared to Bacteria and Eukarya. We report here the structure of a hyperthermophilic virus isolated from an archaeal host found in hot springs in Yellowstone National Park. The sequence of the circular double-stranded DNA viral genome shows that it shares little similarity to other known genes in viruses or other organisms. By comparing the tertiary and quaternary structures of the coat protein of this virus with those of a bacterial and an animal virus, we find conformational relationships among all three, suggesting that some viruses may have a common ancestor that precedes the division into three domains of life >3 billion years ago.
History
DepositionAug 19, 2019-
Header (metadata) releaseSep 25, 2019-
Map releaseSep 25, 2019-
UpdateDec 25, 2019-
Current statusDec 25, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0065
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0065
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20618.png

Downloads & links

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Map

FileDownload / File: emd_20618.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSulfolbus Turreted Icosahedral Virus with Petals at 27 Angstroms Resolution.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
7.5 Å/pix.
x 160 pix.
= 1200. Å		7.5 Å/pix.
x 160 pix.
= 1200. Å		7.5 Å/pix.
x 160 pix.
= 1200. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 7.5 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0065 / Movie #1: 0.0065
Minimum - Maximum-0.044204373 - 0.07067912
Average (Standard dev.)0.00077708025 (±0.0069747516)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 1200.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z7.57.57.5
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z1200.0001200.0001200.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-200-200-200
NX/NY/NZ401401401
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.0440.0710.001

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Supplemental data

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Sample components

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Entire : Sulfolobus turreted icosahedral virus 1

EntireName: Sulfolobus turreted icosahedral virus 1
Components
  • Virus: Sulfolobus turreted icosahedral virus 1

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Supramolecule #1: Sulfolobus turreted icosahedral virus 1

SupramoleculeName: Sulfolobus turreted icosahedral virus 1 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 269145 / Sci species name: Sulfolobus turreted icosahedral virus 1 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Saccharolobus solfataricus (archaea)
Virus shellShell ID: 1 / Diameter: 740.0 Å / T number (triangulation number): 31

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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: 3.5
GridSupport film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Details: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI/PHILIPS CM120T
Image recordingFilm or detector model: KODAK 4489 FILM / Digitization - Scanner: ZEISS SCAI / Average electron dose: 7.5 e/Å2
Electron beamAcceleration voltage: 100 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD

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Image processing

Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 27.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 1330
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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