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- EMDB-1863: Cryo-EM reconstruction of native and expanded Turnip Crinkle virus -

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Basic information

Entry
Database: EMDB / ID: EMD-1863
TitleCryo-EM reconstruction of native and expanded Turnip Crinkle virus
Map data
SampleTurnip crinkle virus:
virus
Keywordsturnip crinkle virus / genomic RNA structure / genome uncoating / ssRNA virus
Function / homologyPlant viruses icosahedral capsid proteins 'S' region signature. / Viral coat protein (S domain) / Icosahedral viral capsid protein, S domain / T=3 icosahedral viral capsid / Viral coat protein subunit / structural molecule activity / viral process / RNA binding / Capsid protein
Function and homology information
Biological speciesTurnip crinkle virus
Methodsingle particle reconstruction / cryo EM / Resolution: 11.5 Å
AuthorsBakker SE / Robottom J / Pearson AR / Stockley PG / Ranson NA
CitationJournal: J Mol Biol / Year: 1986
Title: Structure and assembly of turnip crinkle virus. I. X-ray crystallographic structure analysis at 3.2 A resolution.
Abstract: The structure of turnip crinkle virus has been determined at 3.2 A resolution, using the electron density of tomato bushy stunt virus as a starting point for phase refinement by non-crystallographic ...The structure of turnip crinkle virus has been determined at 3.2 A resolution, using the electron density of tomato bushy stunt virus as a starting point for phase refinement by non-crystallographic symmetry. The structures are very closely related, especially in the subunit arm and S domain, where only small insertions and deletions and small co-ordinate shifts relate one chain to another. The P domains, although quite similar in fold, are oriented somewhat differently with respect to the S domains. Understanding of the structure of turnip crinkle virus has been important for analyzing its assembly, as described in an accompanying paper.
History
DepositionJan 25, 2011-
Header (metadata) releaseJul 9, 2012-
Map releaseJul 9, 2012-
UpdateApr 30, 2014-
Current statusApr 30, 2014Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.9
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.9
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3zx8
  • Surface level: 0.9
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3zx8
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_1863.map.gz / Format: CCP4 / Size: 122.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 320 pix.
= 423.36 Å
1.32 Å/pix.
x 320 pix.
= 423.36 Å
1.32 Å/pix.
x 320 pix.
= 423.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.323 Å
Density
Contour LevelBy AUTHOR: 0.9 / Movie #1: 0.9
Minimum - Maximum-1.74273026 - 4.29223728
Average (Standard dev.)0.24384567 (±1.58257484)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-160-160-160
Dimensions320320320
Spacing320320320
CellA=B=C: 423.36 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3231.3231.323
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z423.360423.360423.360
α/β/γ90.00090.00090.000
start NX/NY/NZ-160-160-159
NX/NY/NZ320320320
MAP C/R/S123
start NC/NR/NS-160-160-160
NC/NR/NS320320320
D min/max/mean-1.7434.2920.244

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Supplemental data

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Sample components

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Entire Turnip crinkle virus

EntireName: Turnip crinkle virus / Number of components: 1 / Oligomeric State: Icosahedral virus
MassTheoretical: 6.8 MDa

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Component #1: virus, Turnip crinkle virus

VirusName: Turnip crinkle virus / a.k.a: Turnip crinkle virus / Class: VIRION / Empty: No / Enveloped: No / Isolate: STRAIN
MassTheoretical: 6.8 MDa
SpeciesSpecies: Turnip crinkle virus
Source (natural)Host Species: Brassica rapa subsp. rapa (turnip)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 2 mg/mL
Buffer solution: 10 mM sodium phosphate pH 7.4, 10 mM magnesium sulphate
pH: 7.4
Support film400 mesh copper grid
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 77 K / Method: Blot 1.6 seconds before plunging
Details: Vitrification instrument: Double sided automated blotter and plunger

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 15 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 50000 X (nominal), 52911 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 3500 nm
Specimen HolderHolder: Gatan 626 / Model: GATAN LIQUID NITROGEN
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionNumber of digital images: 70 / Scanner: ZEISS SCAI / Sampling size: 7 µm

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 18681 / Number of class averages: 331 / Applied symmetry: I (正20面体型対称)
3D reconstructionAlgorithm: Icosahedral / Software: SPIDER / CTF correction: Phase-flipping each particle / Resolution: 11.5 Å / Resolution method: FSC 0.5

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Atomic model buiding

Output model

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