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- EMDB-3020: The Molecular Basis for Flexibility in the Flexible Filamentous P... -

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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 / viral capsid / 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

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Structure visualization

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

EMD-3020-dep...

Downloads & links

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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
Voxel sizeX=Y=Z: 1.05 Å
Density
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

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Supplemental data

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Sample components

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Entire : Bamboo mosaic virus

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

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Supramolecule #1000: Bamboo mosaic virus

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

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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)

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / 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
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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each image
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
DetailsIHRSR

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