[English] 日本語
Yorodumi
- EMDB-1864: Cryo-EM reconstruction of native and expanded Turnip Crinkle virus -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 1864
TitleCryo-EM reconstruction of native and expanded Turnip Crinkle virus
KeywordsTurnip crinkle virus / genomic RNA structure / genome uncoating / ssRNA virus
SampleTurnip crinkle virus
SourceTurnip crinkle virus / virus
Map data3D cryo-EM reconstruction of the expanded form of Turnip Crinkle Virus
Methodsingle particle (icosahedral) reconstruction, at 17 A resolution
AuthorsBakker SE / Robottom J / Pearson AR / Stockley PG / Ranson NA
CitationJ. Mol. Biol., 2012, 417, 65-78

primary. J. Mol. Biol., 2012, 417, 65-78 StrPapers
Isolation of an asymmetric RNA uncoating intermediate for a single-stranded RNA plant virus.
Saskia E Bakker / Robert J Ford / Amy M Barker / Janice Robottom / Keith Saunders / Arwen R Pearson / Neil A Ranson / Peter G Stockley

1. J. Mol. Biol., 1986, 191, 625-638 StrPapers
Structure and assembly of turnip crinkle virus. I. X-ray crystallographic structure analysis at 3.2 A resolution.
J M Hogle / A Maeda / S C Harrison

DateDeposition: Jan 25, 2011 / Header (metadata) release: Jul 9, 2012 / Map release: Jul 9, 2012 / Last update: Jan 25, 2011

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.2
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 3.2
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-3zx9
  • Surface level: 3.2
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


View / / Stereo:
Center
Zoom
Scale
Slabnear <=> far

fix: /
Orientation
Orientation Rotation
Misc. /
Show/hide
Supplemental images

Downloads & links

-
Map

Fileemd_1864.map.gz (map file in CCP4 format, 54001 KB)
Projections & slicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
240 pix
1.89 A/pix
= 453.6 A
240 pix
1.89 A/pix
= 453.6 A
240 pix
1.89 A/pix
= 453.6 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.89 A
Density
Contour Level:3.2 (by author), 3.2 (movie #1):
Minimum - Maximum-1.86774302 - 4.17278814
Average (Standard dev.)0.16210388 (1.48636842)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions240240240
Origin-120-120-120
Limit119119119
Spacing240240240
CellA=B=C: 453.6 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/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
alpha/beta/gamma90.00090.00090.000
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

-
Supplemental data

-
Sample components

-
Entire Turnip crinkle virus

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

-
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 / virus
Source (natural)Host Species: Brassica rapa subsp. rapa / plant / image: Brassica rapa
Shell #1Name of element: Expanded / Diameter: 380 A / T number(triangulation number): 3

+
Experimental details

-
Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 3 mg/ml / Buffer solution: 100 mM Tris pH 8.5, 5 mM EDTA / pH: 8.5
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

-
Electron microscopy imaging

ImagingMicroscope: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 15 e/A2 / 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

-
Image acquisition

Image acquisitionNumber of digital images: 41 / Scanner: OTHER / Sampling size: 10 microns

-
Image processing

ProcessingMethod: single particle (icosahedral) reconstruction / Number of projections: 5121 / Number of class averages: 110 / Applied symmetry: I (icosahedral)
3D reconstructionAlgorithm: Icosahedral / Software: SPIDER / CTF correction: Phase-flipping each particle / Resolution: 17 A / Resolution method: FSC 0.5

-
Atomic model buiding

Output model

+
About Yorodumi

-
News

-
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

-
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

+
Mar 3, 2016. Presentation (PDF format) at IPR seminar on Feb 19.

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

Read more