[English] 日本語
- EMDB-8603: Sub-tomogram average of the archaellar motor in Thermococcus koda... -

Open data

ID or keywords:


no data

Basic information

Database: EMDB / ID: 8603
TitleSub-tomogram average of the archaellar motor in Thermococcus kodakaraensis
SampleArchaellar motor
SourceThermococcus kodakaraensis / archaea / thermophilic
Map data
Methodsubtomogram averaging, at 40 Å resolution
AuthorsChang Y-W / Kjaer A / Briegel A / Oikonomou CM / Jensen GJ
CitationEMBO Rep., 2017, 18, 1660-1670

EMBO Rep., 2017, 18, 1660-1670 Yorodumi Papers
Morphology of the archaellar motor and associated cytoplasmic cone in.
Ariane Briegel / Catherine M Oikonomou / Yi-Wei Chang / Andreas Kjær / Audrey N Huang / Ki Woo Kim / Debnath Ghosal / Hong H Nguyen / Dorothy Kenny / Rachel R Ogorzalek Loo / Robert P Gunsalus / Grant J Jensen

DateDeposition: Feb 13, 2017 / Header (metadata) release: Feb 22, 2017 / Map release: Jul 26, 2017 / Last update: Feb 14, 2018

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 0.067
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.067
  • Imaged by UCSF CHIMERA
  • Download
3D viewer

View / / Stereo:
Slabnear <=> far

fix: /
Orientation Rotation
Misc. /
Supplemental images

Downloads & links


Fileemd_8603.map.gz (map file in CCP4 format, 1001 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
50 pix
6.6 Å/pix.
= 330. Å
100 pix
6.6 Å/pix.
= 660. Å
50 pix
6.6 Å/pix.
= 330. Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 6.6 Å
Contour Level:0.067 (by author), 0.067 (movie #1):
Minimum - Maximum0.012801021 - 0.1403
Average (Standard dev.)0.05666378 (0.01550041)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA: 330 Å / B: 660 Å / C: 330 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z6.66.66.6
M x/y/z5010050
origin x/y/z0.0000.0000.000
length x/y/z330.000660.000330.000
start NX/NY/NZ000
MAP C/R/S123
start NC/NR/NS000
D min/max/mean0.0130.1400.057

Supplemental data

Sample components

Entire Archaellar motor

EntireName: Archaellar motor / Number of components: 1

Component #1: protein, Archaellar motor

ProteinName: Archaellar motor / Recombinant expression: No
SourceSpecies: Thermococcus kodakaraensis / archaea / thermophilic

Experimental details

Sample preparation

Specimen statecell
Sample solutionpH: 7
VitrificationCryogen name: ETHANE-PROPANE MIXTURE

Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.5 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

Image processing

ProcessingMethod: subtomogram averaging / Applied symmetry: C20 (20 fold cyclic)
3D reconstructionSoftware: TOMO3D / Resolution: 40 Å / Resolution method: OTHER

About Yorodumi


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


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