[English] 日本語
Yorodumi
- EMDB-8657: Zika virus-infected Vero E6 cell at 48 hpi, showing spherule pore... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 8657
TitleZika virus-infected Vero E6 cell at 48 hpi, showing spherule pore opening to cytoplasm
SampleZika virus-infected Vero E6 cell at 48 hpi
SourceChlorocebus aethiops / mammal / ミドリザル
Zika virus / virus / ジカウイルス
Map dataTomogram showing pore opening from spherule to cytoplasm in Zika virus infected Vero E6 cell at 48 hpi
Methodelectron tomography
AuthorsRossignol ED / Bullitt E
CitationCell. Microbiol., 2017, 19

Cell. Microbiol., 2017, 19 StrPapers
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_8657.map.gz (map file in CCP4 format, 49124 KB)
Voxel sizeX=Y=Z: 10.86 Å
Density
Contour Level:30 (by emdb)
Minimum - Maximum-128 - 127
Average (Standard dev.)-25.508686 (27.370737)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions70870898
Origin-26-47939
Limit681228136
Spacing70870898
CellA: 7688.88 Å / B: 7688.88 Å / C: 1064.2799 Å
α=β=γ: 90 deg.

CCP4 map header:

modeenvelope stored as signed bytes (from -128 lowest to 127 highest)
Å/pix. X/Y/Z10.8610.8610.86
M x/y/z70870898
origin x/y/z0.0000.0000.000
length x/y/z7688.8807688.8801064.280
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-479-2639
NC/NR/NS70870898
D min/max/mean-128.000127.000-25.509

-
Supplemental data

-
Sample components

-
Entire Zika virus-infected Vero E6 cell at 48 hpi

EntireName: Zika virus-infected Vero E6 cell at 48 hpi
Details: Cells were infected at a multiplicity of infection of 5 for 48 hours. Cells were conventionally fixed and embedded in TAAB Epon. Tomogram includes 2 joined serial sections, each a dual-axis tomogram.
Number of components: 3

-
Component #1: cellular-component, Zika virus-infected Vero E6 cell at 48 hpi

Cellular-componentName: Zika virus-infected Vero E6 cell at 48 hpi
Details: Cells were infected at a multiplicity of infection of 5 for 48 hours. Cells were conventionally fixed and embedded in TAAB Epon. Tomogram includes 2 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
Staining1% OsO4, 1.5% KFeCN6, 1% UA. 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: 214 / Details: Collected using SerialEM
3D reconstructionAlgorithm: EXACT BACK PROJECTION / Software: IMOD

+
About Yorodumi

-
News

-
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)

+
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

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