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- EMDB-5142: Ab initio reconstruction of the avian polyomavirus via the asymme... -

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Basic information

Entry
Database: EMDB / ID: 5142
TitleAb initio reconstruction of the avian polyomavirus via the asymmetric random-model method
Map dataThe avian polyomavirus
SampleAvian polyomavirus:
virus
Keywordsrandom-model method / ab initio reconstruction / avian polyomavirus
SourceAvian polyomavirus (Avian polyomavirus)
Methodsingle particle reconstruction / cryo EM / 35 Å resolution
AuthorsSanz E / Stewart AB / Belnap DM
CitationJournal: J. Struct. Biol. / Year: 2010
Title: The random-model method enables ab initio 3D reconstruction of asymmetric particles and determination of particle symmetry.
Authors: Eduardo Sanz-García / Aaron B Stewart / David M Belnap
Abstract: Model-based, 3D reconstruction techniques depend on reliable starting models. We present an extension of the random-model method (RMM) that allows the ab initio generation of suitable starting models ...Model-based, 3D reconstruction techniques depend on reliable starting models. We present an extension of the random-model method (RMM) that allows the ab initio generation of suitable starting models directly from un-averaged, experimental images of asymmetric or symmetric particles. Therefore, the asymmetric RMM can also be used to determine point-group symmetry. The procedure is facilitated by the use of (a) variable angular step-sizes during iterative origin and orientation searches, (b) high numbers of particle images, and (c) highly defocused images. The method is inhibited by mixed-handedness orientation assignments and by particles with inconspicuous features. For symmetric particles, symmetric RMMs can overcome these deficiencies.
DateDeposition: Nov 21, 2009 / Header (metadata) release: Apr 26, 2010 / Map release: Apr 26, 2010 / Last update: Jun 21, 2010

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.722
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.722
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_5142.map.gz (map file in CCP4 format, 193091 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
367 pix
1.63 Å/pix.
= 598.21 Å
367 pix
1.63 Å/pix.
= 598.21 Å
367 pix
1.63 Å/pix.
= 598.21 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.63 Å
Density
Contour Level:0.722 (by author), 0.722 (movie #1):
Minimum - Maximum-2.49513 - 3.13667
Average (Standard dev.)0.000389735 (0.489641)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions367367367
Origin-183-183-183
Limit183183183
Spacing367367367
CellA=B=C: 598.21 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.631.631.63
M x/y/z367367367
origin x/y/z0.0000.0000.000
length x/y/z598.210598.210598.210
α/β/γ90.00090.00090.000
start NX/NY/NZ-34-26-72
NX/NY/NZ6953145
MAP C/R/S123
start NC/NR/NS-183-183-183
NC/NR/NS367367367
D min/max/mean-2.4953.1370.000

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Supplemental data

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Sample components

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Entire Avian polyomavirus

EntireName: Avian polyomavirus / Number of components: 1

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Component #1: virus, Avian polyomavirus

VirusName: Avian polyomavirus / a.k.a: Avian polyomavirus / Class: VIRION / Empty: No / Enveloped: No / Isolate: STRAIN
SpeciesSpecies: Avian polyomavirus (Avian polyomavirus)
Source (natural)Host Species: Aves / Host category: VERTEBRATES
Shell #1Name of element: VP1 / Diameter: 520 Å / T number(triangulation number): 7

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
VitrificationInstrument: FEI VITROBOT / Cryogen name: ETHANE / Details: Vitrification instrument: Vitrobot

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
LensMagnification: 39000 X (nominal) / Imaging mode: BRIGHT FIELD / Defocus: 700 - 4900 nm
Specimen HolderHolder: Eucentric / Model: GATAN LIQUID NITROGEN
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionScanner: NIKON SUPER COOLSCAN 9000 / Sampling size: 6.3 microns

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 4198 / Applied symmetry: C1 (asymmetric)
3D reconstructionAlgorithm: Projection matching / Software: PFT3DR, Bsoft / CTF correction: None
Details: Random-model method. Angular step-size was initially set to 20 deg. in the first iteration and gradually decreased by 0.19 deg. in each successive iteration, until a lower limit of 1 deg. was reached.
Resolution: 35 Å / Resolution method: FSC 0.5

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