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- EMDB-5039: Cryo-EM reconstruction of the giant Mimivirus using C5 symmetry -

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Basic information

Entry
Database: EMDB / ID: EMD-5039
TitleCryo-EM reconstruction of the giant Mimivirus using C5 symmetry
Map dataThis is a volume map of Mimivirus reconstrument averaged by C5 symmetry
Sample
  • Sample: Mimivirus
  • Virus: Acanthamoeba polyphaga mimivirus
KeywordsMimivirus / Acanthamoeba polyphaga / cryo-electron microscope / atomic force microscope / fiber / digestion / starfish-shaped feature / 5-fold symmetry / nucleocapsid / major capsid protein / capsomer arrangement
Biological speciesAcanthamoeba polyphaga mimivirus
Methodsingle particle reconstruction / cryo EM / Resolution: 65.0 Å
AuthorsXiao C / Kuznetsov YG / Sun S / Hafenstein SL / Kostyuchenko VA / Chipman PR / Suzan-Monti M / Raoult D / McPherson A / Rossmann MG
CitationJournal: PLoS Biol / Year: 2009
Title: Structural studies of the giant mimivirus.
Authors: Chuan Xiao / Yurii G Kuznetsov / Siyang Sun / Susan L Hafenstein / Victor A Kostyuchenko / Paul R Chipman / Marie Suzan-Monti / Didier Raoult / Alexander McPherson / Michael G Rossmann /
Abstract: Mimivirus is the largest known virus whose genome and physical size are comparable to some small bacteria, blurring the boundary between a virus and a cell. Structural studies of Mimivirus have been ...Mimivirus is the largest known virus whose genome and physical size are comparable to some small bacteria, blurring the boundary between a virus and a cell. Structural studies of Mimivirus have been difficult because of its size and long surface fibers. Here we report the use of enzymatic digestions to remove the surface fibers of Mimivirus in order to expose the surface of the viral capsid. Cryo-electron microscopy (cryoEM) and atomic force microscopy were able to show that the 20 icosahedral faces of Mimivirus capsids have hexagonal arrays of depressions. Each depression is surrounded by six trimeric capsomers that are similar in structure to those in many other large, icosahedral double-stranded DNA viruses. Whereas in most viruses these capsomers are hexagonally close-packed with the same orientation in each face, in Mimivirus there are vacancies at the systematic depressions with neighboring capsomers differing in orientation by 60 degrees . The previously observed starfish-shaped feature is well-resolved and found to be on each virus particle and is associated with a special pentameric vertex. The arms of the starfish fit into the gaps between the five faces surrounding the unique vertex, acting as a seal. Furthermore, the enveloped nucleocapsid is accurately positioned and oriented within the capsid with a concave surface facing the unique vertex. Thus, the starfish-shaped feature and the organization of the nucleocapsid might regulate the delivery of the genome to the host. The structure of Mimivirus, as well as the various fiber components observed in the virus, suggests that the Mimivirus genome includes genes derived from both eukaryotic and prokaryotic organisms. The three-dimensional cryoEM reconstruction reported here is of a virus with a volume that is one order of magnitude larger than any previously reported molecular assembly studied at a resolution of equal to or better than 65 Angstroms.
History
DepositionDec 17, 2008-
Header (metadata) releaseMay 5, 2009-
Map releaseMay 5, 2009-
UpdateSep 23, 2011-
Current statusSep 23, 2011Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3000
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 3000
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_5039.map.gz / Format: CCP4 / Size: 300.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a volume map of Mimivirus reconstrument averaged by C5 symmetry
Voxel sizeX=Y=Z: 15.875 Å
Density
Contour LevelBy EMDB: 2700.0 / Movie #1: 3000
Minimum - Maximum-2301.139999999999873 - 4785.079999999999927
Average (Standard dev.)-579.495999999999981 (±1759.369999999999891)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-216-216-216
Dimensions432432432
Spacing432432432
CellA=B=C: 6858 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z15.87515.87515.875
M x/y/z432432432
origin x/y/z0.0000.0000.000
length x/y/z6858.0006858.0006858.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-20-28-19
NX/NY/NZ415638
MAP C/R/S123
start NC/NR/NS-216-216-216
NC/NR/NS432432432
D min/max/mean-2301.1364785.077-579.496

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Supplemental data

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Sample components

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Entire : Mimivirus

EntireName: Mimivirus
Components
  • Sample: Mimivirus
  • Virus: Acanthamoeba polyphaga mimivirus

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Supramolecule #1000: Mimivirus

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

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Supramolecule #1: Acanthamoeba polyphaga mimivirus

SupramoleculeName: Acanthamoeba polyphaga mimivirus / type: virus / ID: 1 / Name.synonym: Mimivirus / NCBI-ID: 212035 / Sci species name: Acanthamoeba polyphaga mimivirus / Database: NCBI / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No / Syn species name: Mimivirus
Host (natural)Organism: Acanthamoeba polyphaga (eukaryote) / synonym: PROTOZOA
Virus shellShell ID: 1 / Name: Mimivirus capsid / Diameter: 5000 Å

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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: 7.4 / Details: PBS (137 mM NaCl, 10 mM Phosphate, 2.7 mM KCl)
GridDetails: 200 Copper grid
VitrificationCryogen name: ETHANE / Chamber temperature: 80 K / Instrument: REICHERT-JUNG PLUNGER
Details: Vitrification instrument: Reichert plunger. Using Quantifoil S7 slash 2 grid
Method: Blot for 1 seconds before plunging

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Electron microscopy

MicroscopeFEI/PHILIPS CM300FEG/T
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 24423 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus min: 4.505 µm / Nominal magnification: 24000
Sample stageSpecimen holder: Side entry liquid nitrogen-cooled cryo specimen holder
Specimen holder model: GATAN LIQUID NITROGEN
TemperatureAverage: 80 K
Alignment procedureLegacy - Astigmatism: objective lens astigmatism was corrected at 98,000 times magnification
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 38.1 µm / Average electron dose: 20 e/Å2 / Details: 6.35 um scanned then bined 6 times to 38.1 um / Bits/pixel: 16
Tilt angle min0
Tilt angle max0

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Image processing

CTF correctionDetails: Each particle
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 65.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Frealign / Number images used: 30919

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