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- EMDB-5142: Ab initio reconstruction of the avian polyomavirus via the asymme... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-5142 | |||||||||
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Title | Ab initio reconstruction of the avian polyomavirus via the asymmetric random-model method | |||||||||
![]() | The avian polyomavirus | |||||||||
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![]() | random-model method / ab initio reconstruction / avian polyomavirus | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 35.0 Å | |||||||||
![]() | Sanz E / Stewart AB / Belnap DM | |||||||||
![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 91.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 8.1 KB 8.1 KB | Display Display | ![]() |
Images | ![]() ![]() ![]() | 77.5 KB 6.3 KB 489.9 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | The avian polyomavirus | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.63 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Avian polyomavirus
Entire | Name: ![]() |
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Components |
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-Supramolecule #1000: Avian polyomavirus
Supramolecule | Name: Avian polyomavirus / type: sample / ID: 1000 / Number unique components: 1 |
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-Supramolecule #1: Avian polyomavirus
Supramolecule | Name: 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 |
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Host (natural) | Organism: ![]() |
Virus shell | Shell ID: 1 / Name: VP1 / Diameter: 520 Å / T number (triangulation number): 7 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Vitrification | Cryogen name: ETHANE / Instrument: OTHER / Details: Vitrification instrument: Vitrobot |
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Electron microscopy
Microscope | FEI TECNAI F30 |
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Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 6.3 µm |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.9 µm / Nominal defocus min: 0.7 µm / Nominal magnification: 39000 |
Sample stage | Specimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | ![]() Model: Tecnai F30 / Image courtesy: FEI Company |
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Image processing
CTF correction | Details: None |
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Final reconstruction | Algorithm: 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 |