[English] 日本語
- EMDB-9766: Doublet microtubule of fap45 null mutant -

Open data

ID or keywords:


no data

Basic information

Database: EMDB / ID: 9766
TitleDoublet microtubule of fap45 null mutant
Map datafap45_DMT
Sampleaxoneme of Chlamydomonas reinhardtii:
SourceChlamydomonas reinhardtii (plant)
Methodsubtomogram averaging / cryo EM / 39.6 Å resolution
AuthorsOwa M / Uchihashi T / Yanagisawa H / Yamano T / Iguchi H / Fukuzawa H / Wakabayashi K / Ando T / Kikkawa M
CitationJournal: To Be Published
Title: Inner lumen proteins stabilize doublet microtubules in cilia/flagella
Authors: Owa M / Uchihashi T / Yanagisawa H / Yamano T / Iguchi H / Fukuzawa H / Wakabayashi K / Ando T / Kikkawa M
DateDeposition: Dec 28, 2018 / Header (metadata) release: Jan 30, 2019 / Map release: Jan 30, 2019 / Last update: Jan 30, 2019

Structure visualization

  • Surface view colored by cylindrical radius
  • Surface level: 60
  • Imaged by UCSF Chimera
  • Download
  • Surface view with section colored by density value
  • Surface level: 60
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
Supplemental images

Downloads & links


Fileemd_9766.map.gz (map file in CCP4 format, 32001 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
200 pix
7.1 Å/pix.
= 1420. Å
200 pix
7.1 Å/pix.
= 1420. Å
200 pix
7.1 Å/pix.
= 1420. Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 7.1 Å
Contour Level:60.0 (by author), 60 (movie #1):
Minimum - Maximum-384.406830000000014 - 388.135620000000017
Average (Standard dev.)-9.983328 (48.821674000000002)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 1420.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z7.17.17.1
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z1420.0001420.0001420.000
start NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
D min/max/mean-384.407388.136-9.983

Supplemental data

Sample components

Entire axoneme of Chlamydomonas reinhardtii

EntireName: axoneme of Chlamydomonas reinhardtii / Number of components: 1

Component #1: cellular-component, axoneme of Chlamydomonas reinhardtii

Cellular-componentName: axoneme of Chlamydomonas reinhardtii / Recombinant expression: No
SourceSpecies: Chlamydomonas reinhardtii (plant) / Strain: fap45

Experimental details

Sample preparation

SpecimenSpecimen state: filament / Method: cryo EM
Sample solutionSpecimen conc.: 0.02 mg/ml / pH: 7.4
VitrificationCryogen name: ETHANE

Electron microscopy imaging

ImagingMicroscope: JEOL 3100FFC
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1 e/Å2 / Illumination mode: OTHER
LensImaging mode: DIFFRACTION
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

Image processing

ProcessingMethod: subtomogram averaging / Applied symmetry: C1 (asymmetric) / Number of subtomograms: 2200
3D reconstructionResolution: 39.6 Å / Resolution method: FSC 0.5 CUT-OFF

About Yorodumi


Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.: Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator

External links: EMDB at EBI / Contact to PDBj

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

Read more


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