[English] 日本語
Yorodumi
- EMDB-5142: Ab initio reconstruction of the avian polyomavirus via the asymme... -

+
Open data


ID or keywords:

Loading...

-
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

-
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
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

400_5142.gif

emd_5142_1.tif

Downloads & links

-
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
Projections & slices

Image control

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

Histogram

Histogram (log scale)
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

-
Supplemental data

-
Sample components

-
Entire : Avian polyomavirus

EntireName: Avian polyomavirus
Components
  • Sample: Avian polyomavirus
  • Virus: Avian polyomavirus

-
Supramolecule #1000: Avian polyomavirus

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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

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

-
Electron microscopy

MicroscopeFEI TECNAI F30
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 6.3 µm
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / 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
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more