[English] 日本語
Yorodumi
- EMDB-8655: Zika virus-infected Vero E6 cell at 20 hpi: dual-axis tilt series... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 8655
TitleZika virus-infected Vero E6 cell at 20 hpi: dual-axis tilt series tomogram from 3 serial sections
SampleZika virus-infected Vero E6 cell at 20 hpi
SourceChlorocebus aethiops / mammal / ミドリザル
Zika virus / virus / ジカウイルス
Map dataZika virus-infected cell at 20 hpi. High pressure frozen/freeze substituted sample, 3 serial sections, dual axis tomogram
Methodelectron tomography
AuthorsRossignol ED / Bullitt E
CitationCell. Microbiol., 2017, 19

Cell. Microbiol., 2017, 19 Yorodumi Papers
Zika virus induced cellular remodelling.
Evan D Rossignol / Kristen N Peters / John H Connor / Esther Bullitt

DateDeposition: Mar 28, 2017 / Header (metadata) release: Apr 5, 2017 / Map release: Apr 5, 2017 / Last update: Jul 26, 2017

-
Structure visualization

Movie
  • Simplified surface model
  • Imaged by Jmol
  • Download
3D viewer


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

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

Downloads & links

-
Map

Fileemd_8655.map.gz (map file in CCP4 format, 1570264 KB)
Voxel sizeX=Y=Z: 10.86 Å
Density
Contour Level:50 (by emdb)
Minimum - Maximum-114 - 127
Average (Standard dev.)6.2236724 (25.568787)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions21782246321
Origin0054
Limit21772245374
Spacing22462178321
CellA: 24391.559 Å / B: 23653.08 Å / C: 3486.0598 Å
α=β=γ: 90 deg.

CCP4 map header:

modeenvelope stored as signed bytes (from -128 lowest to 127 highest)
Å/pix. X/Y/Z10.85999955476410.8610.86
M x/y/z22462178321
origin x/y/z0.0000.0000.000
length x/y/z24391.55923653.0803486.060
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS0054
NC/NR/NS22462178321
D min/max/mean-114.000127.0006.224

-
Supplemental data

-
Sample components

-
Entire Zika virus-infected Vero E6 cell at 20 hpi

EntireName: Zika virus-infected Vero E6 cell at 20 hpi
Details: Cells were infected at a multiplicity of infection of 5 for 20 hours. Cells were fixed, scraped, pelleted, high-pressure frozen/freeze substituted, and embedded in TAAB Epon. Tomogram includes 3 joined serial sections, each a dual-axis tomogram.
Number of components: 3

-
Component #1: cellular-component, Zika virus-infected Vero E6 cell at 20 hpi

Cellular-componentName: Zika virus-infected Vero E6 cell at 20 hpi
Details: Cells were infected at a multiplicity of infection of 5 for 20 hours. Cells were fixed, scraped, pelleted, high-pressure frozen/freeze substituted, and embedded in TAAB Epon. Tomogram includes 3 joined serial sections, each a dual-axis tomogram.
Recombinant expression: No

-
Component #2: cellular-component, Vero E6 cell

Cellular-componentName: Vero E6 cell / Recombinant expression: No
SourceSpecies: Chlorocebus aethiops / mammal / ミドリザル / Strain: Vero E6

-
Component #3: virus, Zika virus

VirusName: Zika virus
SpeciesSpecies: Zika virus / virus / ジカウイルス / Strain: PRVABC59

-
Experimental details

-
Sample preparation

Specimen statecell
Sample solutionpH: 7.4
StainingHPF/FS stain of 0.1% UA, 0.1% tannic acid. Post-section stain of 4% UA, 0.2% Reynold's lead citrate
VitrificationCryogen name: NONE

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 160 kV / Electron dose: 30 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: TVIPS TEMCAM-F416 (4k x 4k)

-
Image processing

ProcessingMethod: electron tomography / Number of sections: 693 / Details: Collected using SerialEM
3D reconstructionAlgorithm: EXACT BACK PROJECTION / Software: IMOD

+
About Yorodumi

-
News

-
Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

  • Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
  • Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

-
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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
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)

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