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- EMDB-5584: Life in the extremes: atomic structure of Sulfolobus Turreted Ico... -

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Basic information

Entry
Database: EMDB / ID: EMD-5584
TitleLife in the extremes: atomic structure of Sulfolobus Turreted Icosahedral Virus
Map dataReconstruction of mature STIV
Sample
  • Sample: Mature Sulfolobus Turreted Icosahedral Virus
  • Virus: Sulfolobus turreted icosahedral virus
KeywordsVirus assembly / Evolution / Electron microscopy / Archaea
Function / homologyviral capsid / Coat protein / Uncharacterized protein / Uncharacterized protein
Function and homology information
Biological speciesSulfolobus turreted icosahedral virus
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsVeesler D / Ng TS / Sendamarai AK / Eilers BJ / Lawrence CM / Lok SM / Young MJ / Johnson JE / Fu CY
CitationJournal: Proc Natl Acad Sci U S A / Year: 2013
Title: Atomic structure of the 75 MDa extremophile Sulfolobus turreted icosahedral virus determined by CryoEM and X-ray crystallography.
Authors: David Veesler / Thiam-Seng Ng / Anoop K Sendamarai / Brian J Eilers / C Martin Lawrence / Shee-Mei Lok / Mark J Young / John E Johnson / Chi-yu Fu /
Abstract: Sulfolobus turreted icosahedral virus (STIV) was isolated in acidic hot springs where it infects the archeon Sulfolobus solfataricus. We determined the STIV structure using near-atomic resolution ...Sulfolobus turreted icosahedral virus (STIV) was isolated in acidic hot springs where it infects the archeon Sulfolobus solfataricus. We determined the STIV structure using near-atomic resolution electron microscopy and X-ray crystallography allowing tracing of structural polypeptide chains and visualization of transmembrane proteins embedded in the viral membrane. We propose that the vertex complexes orchestrate virion assembly by coordinating interactions of the membrane and various protein components involved. STIV shares the same coat subunit and penton base protein folds as some eukaryotic and bacterial viruses, suggesting that they derive from a common ancestor predating the divergence of the three kingdoms of life. One architectural motif (β-jelly roll fold) forms virtually the entire capsid (distributed in three different gene products), indicating that a single ancestral protein module may have been at the origin of its evolution.
History
DepositionFeb 18, 2013-
Header (metadata) releaseApr 3, 2013-
Map releaseMay 1, 2013-
UpdateNov 20, 2013-
Current statusNov 20, 2013Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3j31
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3j31
  • Imaged by Jmol
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

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Map

FileDownload / File: emd_5584.map.gz / Format: CCP4 / Size: 3.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of mature STIV
Voxel sizeX=Y=Z: 1.37 Å
Density
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.19078529 - 0.33287722
Average (Standard dev.)-0.00098297 (±0.01407928)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-512-512-512
Dimensions102410241024
Spacing102410241024
CellA: 1402.88 Å / B: 1402.8801 Å / C: 1402.88 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.371.371.37
M x/y/z102410241024
origin x/y/z0.0000.0000.000
length x/y/z1402.8801402.8801402.880
α/β/γ90.00090.00090.000
start NX/NY/NZ-5029166
NX/NY/NZ106122134
MAP C/R/S123
start NC/NR/NS-512-512-512
NC/NR/NS102410241024
D min/max/mean-0.1910.333-0.001

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Supplemental data

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Sample components

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Entire : Mature Sulfolobus Turreted Icosahedral Virus

EntireName: Mature Sulfolobus Turreted Icosahedral Virus
Components
  • Sample: Mature Sulfolobus Turreted Icosahedral Virus
  • Virus: Sulfolobus turreted icosahedral virus

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Supramolecule #1000: Mature Sulfolobus Turreted Icosahedral Virus

SupramoleculeName: Mature Sulfolobus Turreted Icosahedral Virus / type: sample / ID: 1000 / Number unique components: 5
Molecular weightTheoretical: 75 MDa

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Supramolecule #1: Sulfolobus turreted icosahedral virus

SupramoleculeName: Sulfolobus turreted icosahedral virus / type: virus / ID: 1 / NCBI-ID: 269145 / Sci species name: Sulfolobus turreted icosahedral virus / Sci species strain: Isolate YNPRC179 / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Sulfolobus solfataricus (archaea) / Strain: 2-2-12 / synonym: ARCHAEA
Molecular weightTheoretical: 75 MDa
Virus shellShell ID: 1 / Name: B345-A223 / Diameter: 730 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
Details: 23 mM KH2PO4, 19 mM (NH4)2SO4, 1 mM MgSO4, 2 mM CaCl2
GridDetails: glow-discharged C-flat holey carbon grids (CF-2/2-4C, Protochips)
VitrificationCryogen name: ETHANE / Chamber temperature: 94 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification carried out at room temperature

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 102189 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder: Nitrogen cooled / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
TemperatureAverage: 90 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 103,000 times magnification
DetailsNanoprobe mode was used
DateMar 30, 2011
Image recordingCategory: CCD / Film or detector model: FEI FALCON I (4k x 4k) / Number real images: 878 / Average electron dose: 18 e/Å2
Tilt angle min0
Tilt angle max0
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each particle
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: OTHER / Software - Name: Frealign
Details: The final reconstruction was sharpened with a negative temperature factor of 400A2.
Number images used: 8903

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Atomic model buiding 1

Initial modelPDB ID:
SoftwareName: CNS
DetailsPositional (xyz) minimization and isotropic B factor refinement. Real space refinement was also carried out using Coot.
RefinementSpace: RECIPROCAL
Output model

PDB-3j31:
Life in the extremes: atomic structure of Sulfolobus Turreted Icosahedral Virus

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Atomic model buiding 2

Initial modelPDB ID:
SoftwareName: CNS
DetailsPositional (xyz) minimization and isotropic B factor refinement. Real space refinement was also carried out using Coot. Only the N-terminal domain was refined using CNS (residues 3-134). The C-terminal domain (residues 135-222) was only rigid-body fit using Coot and an arbitrary B-factor value of 150 A2 was assigned to it.
RefinementSpace: RECIPROCAL
Output model

PDB-3j31:
Life in the extremes: atomic structure of Sulfolobus Turreted Icosahedral Virus

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