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- EMDB-6221: Refined structure of lemon-shaped virus His1 using Cryo-ET subtom... -

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Basic information

Entry
Database: EMDB / ID: EMD-6221
TitleRefined structure of lemon-shaped virus His1 using Cryo-ET subtomogram averaging
Map dataRefined C1 reconstruction of His1
Sample
  • Sample: Lemon-shaped archaeal virus His1
  • Virus: Lemon-shaped archaeal virus His1
KeywordsLemon-shaped Virus / Tail Organization / Electron Cryo-Tomography / Subtomogram averaging / Dissociation
Biological speciesLemon-shaped archaeal virus His1
Methodsubtomogram averaging / cryo EM / Resolution: 28.0 Å
AuthorsHong C / Pietila MK / Fu C / Schmid MF / Bamford DH / Chiu W
CitationJournal: Proc Natl Acad Sci U S A / Year: 2015
Title: Lemon-shaped halo archaeal virus His1 with uniform tail but variable capsid structure.
Authors: Chuan Hong / Maija K Pietilä / Caroline J Fu / Michael F Schmid / Dennis H Bamford / Wah Chiu /
Abstract: Lemon-shaped viruses are common in nature but so far have been observed to infect only archaea. Due to their unusual shape, the structures of these viruses are challenging to study and therefore ...Lemon-shaped viruses are common in nature but so far have been observed to infect only archaea. Due to their unusual shape, the structures of these viruses are challenging to study and therefore poorly characterized. Here, we have studied haloarchaeal virus His1 using cryo-electron tomography as well as biochemical dissociation. The virions have different sizes, but prove to be extremely stable under various biochemical treatments. Subtomogram averaging of the computationally extracted virions resolved a tail-like structure with a central tail hub density and six tail spikes. Inside the tail there are two cavities and a plug density that separates the tail hub from the interior genome. His1 most likely uses the tail spikes to anchor to host cells and the tail hub to eject the genome, analogous to classic tailed bacteriophages. Upon biochemical treatment that releases the genome, the lemon-shaped virion transforms into an empty tube. Such a dramatic transformation demonstrates that the capsid proteins are capable of undergoing substantial quaternary structural changes, which may occur at different stages of the virus life cycle.
History
DepositionDec 20, 2014-
Header (metadata) releaseFeb 11, 2015-
Map releaseFeb 11, 2015-
UpdateAug 26, 2015-
Current statusAug 26, 2015Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 4
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

400_6221.gif

Downloads & links

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Map

FileDownload / File: emd_6221.map.gz / Format: CCP4 / Size: 122.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRefined C1 reconstruction of His1
Voxel sizeX=Y=Z: 4.52 Å
Density
Contour LevelBy AUTHOR: 4.0 / Movie #1: 4
Minimum - Maximum-5.74911404 - 15.27153015
Average (Standard dev.)0.0 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-1033
Dimensions320320320
Spacing320320320
CellA=B=C: 1446.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.524.524.52
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z1446.4001446.4001446.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS3-103
NC/NR/NS320320320
D min/max/mean-5.74915.272-0.000

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Supplemental data

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Sample components

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Entire : Lemon-shaped archaeal virus His1

EntireName: Lemon-shaped archaeal virus His1
Components
  • Sample: Lemon-shaped archaeal virus His1
  • Virus: Lemon-shaped archaeal virus His1

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Supramolecule #1000: Lemon-shaped archaeal virus His1

SupramoleculeName: Lemon-shaped archaeal virus His1 / type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: Lemon-shaped archaeal virus His1

SupramoleculeName: Lemon-shaped archaeal virus His1 / type: virus / ID: 1 / Sci species name: Lemon-shaped archaeal virus His1 / Database: NCBI / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Haloarcula hispanica (Halophile) / synonym: ARCHAEA
Virus shellShell ID: 1 / Diameter: 400 Å

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7.2
Details: 50 mM NaCl, 3.5 mM MgCl2, 1 mM KCl, 0.1 mM CaCl2, 50 mM Tris-HCl, pH 7.2
GridDetails: 200 mesh Quantifoil grids, glow discharged for 15 seconds
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 93 K / Instrument: FEI VITROBOT MARK III / Method: Blot for 2 seconds

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Electron microscopy

MicroscopeJEOL 2200FS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 33186 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm / Nominal defocus max: 1.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 25000
Specialist opticsEnergy filter - Name: Omega JEOL / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: -65 ° / Tilt series - Axis1 - Max angle: 65 °
TemperatureMin: 80 K / Max: 93 K / Average: 90 K
Alignment procedureLegacy - Astigmatism: Corrected at 100,000x magnification
DateOct 1, 2012
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Sampling interval: 15 µm / Number real images: 2500 / Average electron dose: 100 e/Å2 / Camera length: 150

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Image processing

Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 28.0 Å / Resolution method: OTHER / Software - Name: IMOD, EMAN, EMAN2, tomohunter
Details: The resolution of the tail portion is 28 Angstrom while the resolution of the flexible lemon body is 51 Angstrom.
Number subtomograms used: 2444
DetailsIteratively refined against the all-vs-all starting model

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