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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: EMD-5142
TitleAb initio reconstruction of the avian polyomavirus via the asymmetric random-model method
Map dataThe avian polyomavirus
Sample
  • Sample: Avian polyomavirus
  • Virus: Avian polyomavirus
Keywordsrandom-model method / ab initio reconstruction / avian polyomavirus
Biological speciesAvian polyomavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 35.0 Å
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.
History
DepositionNov 21, 2009-
Header (metadata) releaseApr 26, 2010-
Map releaseApr 26, 2010-
UpdateJun 21, 2010-
Current statusJun 21, 2010Processing site: RCSB / Status: Released

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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

FileDownload / File: emd_5142.map.gz / Format: CCP4 / Size: 184.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe avian polyomavirus
Voxel sizeX=Y=Z: 1.63 Å
Density
Contour LevelBy AUTHOR: 0.722 / Movie #1: 0.722
Minimum - Maximum-2.49513 - 3.13667
Average (Standard dev.)0.000389735 (±0.489641)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-183-183-183
Dimensions367367367
Spacing367367367
CellA=B=C: 598.21 Å
α=β=γ: 90 °

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
Components
  • Sample: Avian polyomavirus
  • Virus: Avian polyomavirus

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Supramolecule #1000: Avian polyomavirus

SupramoleculeName: Avian polyomavirus / type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: Avian polyomavirus

SupramoleculeName: Avian polyomavirus / type: virus / ID: 1 / Name.synonym: Avian polyomavirus / Sci species name: Avian polyomavirus / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: Avian polyomavirus
Host (natural)Organism: Aves (birds) / synonym: VERTEBRATES
Virus shellShell ID: 1 / Name: VP1 / Diameter: 520 Å / T number (triangulation number): 7

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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

VitrificationCryogen name: ETHANE / Instrument: OTHER / Details: Vitrification instrument: Vitrobot

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Electron microscopy

MicroscopeFEI TECNAI F30
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 4.9 µm / Nominal defocus min: 0.7 µm / Nominal magnification: 39000
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 6.3 µm
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: None
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 35.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: PFT3DR, Bsoft
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.
Number images used: 4198

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