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- EMDB-1864: Cryo-EM reconstruction of native and expanded Turnip Crinkle virus -

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Basic information

Entry
Database: EMDB / ID: EMD-1864
TitleCryo-EM reconstruction of native and expanded Turnip Crinkle virus
Map data3D cryo-EM reconstruction of the expanded form of Turnip Crinkle Virus
Sample
  • Sample: Turnip crinkle virus
  • Virus: Turnip crinkle virus
KeywordsTurnip crinkle virus / genomic RNA structure / genome uncoating / ssRNA virus
Function / homology
Function and homology information


T=3 icosahedral viral capsid / symbiont-mediated suppression of host innate immune response / virus-mediated perturbation of host defense response / structural molecule activity / RNA binding
Similarity search - Function
Plant viruses icosahedral capsid proteins 'S' region signature. / Icosahedral viral capsid protein, S domain / Viral coat protein (S domain) / Viral coat protein subunit
Similarity search - Domain/homology
Biological speciesTurnip crinkle virus
Methodsingle particle reconstruction / cryo EM / Resolution: 17.0 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: 3.2
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 3.2
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3zx9
  • Surface level: 3.2
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3zx9
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_1864.png

Downloads & links

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Map

FileDownload / File: emd_1864.map.gz / Format: CCP4 / Size: 51.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D cryo-EM reconstruction of the expanded form of Turnip Crinkle Virus
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.89 Å/pix.
x 240 pix.
= 453.6 Å		1.89 Å/pix.
x 240 pix.
= 453.6 Å		1.89 Å/pix.
x 240 pix.
= 453.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.89 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.2 / Movie #1: 3.2
Minimum - Maximum-1.86774302 - 4.17278814
Average (Standard dev.)0.16210388 (±1.48636842)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-120-120-120
Dimensions240240240
Spacing240240240
CellA=B=C: 453.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.891.891.89
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z453.600453.600453.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-160-160-159
NX/NY/NZ320320320
MAP C/R/S123
start NC/NR/NS-120-120-120
NC/NR/NS240240240
D min/max/mean-1.8684.1730.162

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Supplemental data

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Sample components

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Entire : Turnip crinkle virus

EntireName: Turnip crinkle virus
Components
  • Sample: Turnip crinkle virus
  • Virus: Turnip crinkle virus

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Supramolecule #1000: Turnip crinkle virus

SupramoleculeName: Turnip crinkle virus / type: sample / ID: 1000 / Oligomeric state: Icosahedral virus / Number unique components: 1
Molecular weightTheoretical: 6.8 MDa

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Supramolecule #1: Turnip crinkle virus

SupramoleculeName: Turnip crinkle virus / type: virus / ID: 1 / Name.synonym: Turnip crinkle virus / NCBI-ID: 11988 / Sci species name: Turnip crinkle virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: Turnip crinkle virus
Host (natural)Organism: Brassica rapa subsp. rapa (turnip)
Molecular weightTheoretical: 6.8 MDa
Virus shellShell ID: 1 / Name: Expanded / Diameter: 380 Å / T number (triangulation number): 3

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration3 mg/mL
BufferpH: 8.5 / Details: 100 mM Tris pH 8.5, 5 mM EDTA
GridDetails: 400 mesh copper grid
VitrificationCryogen name: ETHANE / Chamber temperature: 77 K / Instrument: HOMEMADE PLUNGER
Details: Vitrification instrument: Double sided automated blotter and plunger
Method: Blot 1.6 seconds before plunging

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 10 µm / Number real images: 41 / Average electron dose: 15 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 52911 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Gatan 626 / Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Phase-flipping each particle
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 17.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER / Number images used: 5121
Final two d classificationNumber classes: 110

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