[English] 日本語
Yorodumi
- EMDB-6846: Volta phase contrast cryotomogram of a cryosectioned prometaphase... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 6846
TitleVolta phase contrast cryotomogram of a cryosectioned prometaphase S. pombe cell, strain nda3-KM311
Map dataVolta phase contrast cryotomogram of a cryosectioned prometaphase S. pombe cell, strain nda3-KM311
SampleS. pombe cell, arrested in prometaphase:
SourceSchizosaccharomyces pombe (fission yeast)
Methodelectron tomography / cryo EM
AuthorsCai S / Chen C / Tan Z / Huang Y / Shi J / Gan L
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Cryo-ET reveals the macromolecular reorganization of mitotic chromosomes in vivo.
Authors: Shujun Cai / Chen Chen / Zhi Yang Tan / Yinyi Huang / Jian Shi / Lu Gan
DateDeposition: Nov 21, 2017 / Header (metadata) release: Oct 31, 2018 / Map release: Oct 31, 2018 / Last update: Nov 7, 2018

-
Structure visualization

Movie
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
  • Download
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Supplemental images

emd_6846.png

Downloads & links

-
Map

Fileemd_6846.map.gz (map file in CCP4 format, 4817421 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
184 pix
4.6 Å/pix.
= 846.4 Å		4096 pix
4.6 Å/pix.
= 18841.6 Å		3196 pix
4.6 Å/pix.
= 14701.6 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.6 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-4594.0 - 3240.0
Average (Standard dev.)169.590100000000007 (295.756259999999997)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions40963196184
Origin0.0-901.0112.0
Limit4095.02294.0295.0
Spacing31964096184
CellA: 14701.6 Å / B: 18841.6 Å / C: 846.39996 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Integer*27
Å/pix. X/Y/Z4.64.64.6
M x/y/z31964096184
origin x/y/z0.0000.0000.000
length x/y/z14701.60018841.600846.400
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ240240240
MAP C/R/S123
start NC/NR/NS-9010112
NC/NR/NS31964096184
D min/max/mean-4594.0003240.000169.590

-
Supplemental data

-
Sample components

-
Entire S. pombe cell, arrested in prometaphase

EntireName: S. pombe cell, arrested in prometaphase / Number of components: 1

-
Component #1: cellular-component, S. pombe cell, arrested in prometaphase

Cellular-componentName: S. pombe cell, arrested in prometaphase / Recombinant expression: No
SourceSpecies: Schizosaccharomyces pombe (fission yeast) / Strain: nda3-KM311

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: cell / Method: cryo EM
Sample solutionBuffer solution: yeast-extract supplemented / pH: 7
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.6 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 18000.0 X (nominal), 30400.0 X (calibrated) / Imaging mode: BRIGHT FIELD / Defocus: 500.0 - nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON II (4k x 4k)

-
Image acquisition

Image acquisitionNumber of digital images: 61 / Sampling size: 14 microns
Raw dataEMPIAR-10125 (Title: Cryo-ET reveals the macromolecular reorganization of S. pombe mitotic chromosomes in vivo
Data size: 35.1
Data #1: Tilt series of fission yeast cells and chromatin lysates in various cell cycle states [tilt series])
EMPIAR-10159 (Title: A multi-scale model of the yeast chromosome-segregation system
Data size: 95.4
Data #1: Tilt series, tomograms, and models of cryosections of mitotic budding yeast and reconstituted DASH rings around microtubules [tilt series])

-
Image processing

ProcessingMethod: electron tomography / Number of sections: 61
3D reconstructionAlgorithm: 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

+
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

+
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.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more