[English] 日本語
Yorodumi
- EMDB-3786: Cryo-electron tomography averaged map of microtubule doublet from... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 3786
TitleCryo-electron tomography averaged map of microtubule doublet from p23 mutant Chlamydomonas axoneme
SampleCiliary microtubule doublet with dynein, radial spokes and other binding proteins
SourceChlamydomonas reinhardtii / plant
Map dataSubaverage after subtomogram classification of Chlamydomonas pf23 cilia, based on outer dynein arm structure
Methodsubtomogram averaging, at 50 Å resolution
AuthorsSale WS / Ishikawa T / Yamamoto R / Obbineni JM / Alford LM / Hwang J / Ide T / Owa M / Kon T / Inaba K / Noliyanda J / King SM / Dutcher S
CitationPLoS Genet., 2017, 13, e1006996-e1006996

PLoS Genet., 2017, 13, e1006996-e1006996 Yorodumi Papers
Chlamydomonas DYX1C1/PF23 is essential for axonemal assembly and proper morphology of inner dynein arms.
Ryosuke Yamamoto / Jagan M Obbineni / Lea M Alford / Takahiro Ide / Mikito Owa / Juyeon Hwang / Takahide Kon / Kazuo Inaba / Noliyanda James / Stephen M King / Takashi Ishikawa / Winfield S Sale / Susan K Dutcher

DateDeposition: Jul 6, 2017 / Header (metadata) release: Aug 16, 2017 / Map release: Sep 6, 2017 / Last update: Sep 20, 2017

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: -0.28
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: -0.28
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


View / / Stereo:
Center
Zoom
Scale
Slabnear <=> far

fix: /
Orientation
Orientation Rotation
Misc. /
Show/hide
Supplemental images

Downloads & links

-
Map

Fileemd_3786.map.gz (map file in CCP4 format, 49949 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
232 pix
5.68 Å/pix.
= 1317.76 Å
232 pix
5.68 Å/pix.
= 1317.76 Å
232 pix
5.68 Å/pix.
= 1317.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 5.68 Å
Density
Contour Level:0.001 (by author), -0.28 (movie #1):
Minimum - Maximum-0.76053894 - 0.66737646
Average (Standard dev.)-0.00049874233 (0.098439604)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions232232232
Origin000
Limit231231231
Spacing232232232
CellA=B=C: 1317.76 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.685.685.68
M x/y/z232232232
origin x/y/z0.0000.0000.000
length x/y/z1317.7601317.7601317.760
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS232232232
D min/max/mean-0.7610.667-0.000

-
Supplemental data

-
Sample components

-
Entire Ciliary microtubule doublet with dynein, radial spokes and other ...

EntireName: Ciliary microtubule doublet with dynein, radial spokes and other binding proteins
Number of components: 1

-
Component #1: cellular-component, Ciliary microtubule doublet with dynein, radi...

Cellular-componentName: Ciliary microtubule doublet with dynein, radial spokes and other binding proteins
Recombinant expression: No
SourceSpecies: Chlamydomonas reinhardtii / plant / Strain: pf23
Source (natural)Organelle: cilia

-
Experimental details

-
Sample preparation

Specimen statecell
Sample solutionBuffer solution: 30 mM HEPES, 5 mM MgSO4, 1 mM DTT, 1 mM EGTA, and 50 mM potassium acetate, pH7.4
pH: 7.4
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 298 K / Humidity: 70 % / Details: one side blotting

-
Electron microscopy imaging

ImagingMicroscope: JEOL 2200FS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 0.8 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 20000 X (nominal) / Imaging mode: BRIGHT FIELD / Energy filter: JEOL in-column / Energy window: 0-25 eV
Specimen HolderModel: GATAN LIQUID NITROGEN / Tilt Angle: -60 - 60 deg.
CameraDetector: TVIPS TEMCAM-F416 (4k x 4k)

-
Image processing

ProcessingMethod: subtomogram averaging
3D reconstructionAlgorithm: BACK PROJECTION / Software: SPIDER / Resolution: 50 Å / Resolution method: OTHER
Details: Visual estimation, compared with datasets in the past
Euler angles: 3D cross correlation by Spider

+
About Yorodumi

-
News

-
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

-
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