[English] 日本語
Yorodumi
- EMDB-3020: The Molecular Basis for Flexibility in the Flexible Filamentous P... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-3020
TitleThe Molecular Basis for Flexibility in the Flexible Filamentous Plant Viruses
Map datareconstruction of BaMV
Sample
  • Sample: Bamboo mosaic virus
  • Virus: Bamboo mosaic virus
Keywordshelical polymer / cumulative disorder / plant viruses
Function / homologyPotex/carlavirus coat protein / Viral coat protein / helical viral capsid / ribonucleoprotein complex / structural molecule activity / Coat protein
Function and homology information
Biological speciesBamboo mosaic virus
Methodhelical reconstruction / cryo EM / Resolution: 5.6 Å
AuthorsDiMaio F / Chen CC / Yu X / Frenz B / Hsu YH / Lin NS / Egelman EH
CitationJournal: Nat Struct Mol Biol / Year: 2015
Title: The molecular basis for flexibility in the flexible filamentous plant viruses.
Authors: Frank DiMaio / Chun-Chieh Chen / Xiong Yu / Brandon Frenz / Yau-Heiu Hsu / Na-Sheng Lin / Edward H Egelman /
Abstract: Flexible filamentous plant viruses cause more than half the viral crop damage in the world but are also potentially useful for biotechnology. Structural studies began more than 75 years ago but have ...Flexible filamentous plant viruses cause more than half the viral crop damage in the world but are also potentially useful for biotechnology. Structural studies began more than 75 years ago but have failed, owing to the virion's extreme flexibility. We have used cryo-EM to generate an atomic model for bamboo mosaic virus, which reveals flexible N- and C-terminal extensions that allow deformation while still maintaining structural integrity.
History
DepositionMay 20, 2015-
Header (metadata) releaseJun 10, 2015-
Map releaseJul 22, 2015-
UpdateAug 19, 2015-
Current statusAug 19, 2015Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.09
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.09
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-5a2t
  • Surface level: 0.09
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-5a2t
  • Surface level: 0.09
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-3020-dep...

Downloads & links

-
Map

FileDownload / File: emd_3020.map.gz / Format: CCP4 / Size: 12.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationreconstruction of BaMV
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 100 pix.
= 105. Å		1.05 Å/pix.
x 180 pix.
= 189. Å		1.05 Å/pix.
x 180 pix.
= 189. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09 / Movie #1: 0.09
Minimum - Maximum-0.11456875 - 0.24956317
Average (Standard dev.)-0.01237234 (±0.05178053)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-90-90-50
Dimensions180180100
Spacing180180100
CellA: 188.99998 Å / B: 188.99998 Å / C: 104.99999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z180180100
origin x/y/z0.0000.0000.000
length x/y/z189.000189.000105.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-90-90-50
NC/NR/NS180180100
D min/max/mean-0.1150.250-0.012

-
Supplemental data

-
Sample components

-
Entire : Bamboo mosaic virus

EntireName: Bamboo mosaic virus
Components
  • Sample: Bamboo mosaic virus
  • Virus: Bamboo mosaic virus

-
Supramolecule #1000: Bamboo mosaic virus

SupramoleculeName: Bamboo mosaic virus / type: sample / ID: 1000 / Number unique components: 1

-
Supramolecule #1: Bamboo mosaic virus

SupramoleculeName: Bamboo mosaic virus / type: virus / ID: 1 / NCBI-ID: 35286 / Sci species name: Bamboo mosaic virus / Database: NCBI / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Chenopodium quinoa (quinoa) / synonym: PLANTAE(HIGHER PLANTS)

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

-
Sample preparation

VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
DateNov 1, 2014
Image recordingCategory: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Number real images: 1474 / Average electron dose: 20 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.6 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

DetailsIHRSR
Final reconstructionApplied symmetry - Helical parameters - Δz: 4.0 Å
Applied symmetry - Helical parameters - Δ&Phi: 40.9 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 5.6 Å / Resolution method: OTHER / Software - Name: Spider
CTF correctionDetails: Each image

+
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