[English] 日本語
Yorodumi
- EMDB-4355: Chlamydomonas reinhardtii nuclear pore complex -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 4355
TitleChlamydomonas reinhardtii nuclear pore complex
Map dataElectron density map of the Chlamydomonas reinhardtii Nuclear pore complex
SampleFocus Ion Beam milled Chlamydomonas cells:
SourceChlamydomonas reinhardtii (plant)
Methodsubtomogram averaging / cryo EM / 30 Å resolution
AuthorsMosalaganti S / Albert S / Engel BD / Beck M
CitationJournal: Nat Commun / Year: 2018
Title: In situ architecture of the algal nuclear pore complex.
Authors: Shyamal Mosalaganti / Jan Kosinski / Sahradha Albert / Miroslava Schaffer / Daniela Strenkert / Patrice A Salomé / Sabeeha S Merchant / Jürgen M Plitzko / Wolfgang Baumeister / Benjamin D Engel / Martin Beck
DateDeposition: Mar 31, 2018 / Header (metadata) release: May 23, 2018 / Map release: Jul 4, 2018 / Last update: Jul 4, 2018

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 1
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

Fileemd_4355.map.gz (map file in CCP4 format, 70305 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
260 pix
6.84 Å/pix.
= 1778.4 Å
260 pix
6.84 Å/pix.
= 1778.4 Å
260 pix
6.84 Å/pix.
= 1778.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 6.84 Å
Density
Contour Level:1.0 (by author), 1 (movie #1):
Minimum - Maximum-3.84082 - 6.5159717
Average (Standard dev.)-0.0044762474 (0.35131323)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions260260260
Origin0.0.0.
Limit259.259.259.
Spacing260260260
CellA=B=C: 1778.4 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z6.846.846.84
M x/y/z260260260
origin x/y/z0.0000.0000.000
length x/y/z1778.4001778.4001778.400
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS260260260
D min/max/mean-3.8416.516-0.004

-
Supplemental data

-
Sample components

-
Entire Focus Ion Beam milled Chlamydomonas cells

EntireName: Focus Ion Beam milled Chlamydomonas cells / Number of components: 1

-
Component #1: cellular-component, Focus Ion Beam milled Chlamydomonas cells

Cellular-componentName: Focus Ion Beam milled Chlamydomonas cells / Recombinant expression: No
SourceSpecies: Chlamydomonas reinhardtii (plant)

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: cell / Method: cryo EM
Sample solutionpH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: OTHER

-
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: 2.5 e/Å2 / Illumination mode: OTHER
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

-
Image processing

ProcessingMethod: subtomogram averaging / Number of subtomograms: 624
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF

+
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