[English] 日本語
Yorodumi
- EMDB-6510: Docking complex-independent alignment of outer dynein arms with 2... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-6510
TitleDocking complex-independent alignment of outer dynein arms with 24-nm periodicity
Map dataStreptavidin-labeled DC2-M412BCCP axoneme
Sample
  • Sample: Streptavidin-labeled ODA structure from DC2-M412BCCP axoneme
  • Organelle or cellular component: axoneme
Keywordscilia and flagella / axoneme / outer dynein arm / docking complex
Biological speciesChlamydomonas reinhardtii (plant)
Methodsubtomogram averaging / cryo EM / Resolution: 47.0 Å
AuthorsOda T / Abe T / Yanagisawa H / Kikkawa M
CitationJournal: J Cell Sci / Year: 2016
Title: Docking-complex-independent alignment of Chlamydomonas outer dynein arms with 24-nm periodicity in vitro.
Authors: Toshiyuki Oda / Tatsuki Abe / Haruaki Yanagisawa / Masahide Kikkawa /
Abstract: The docking complex is a molecular complex necessary for assembly of outer dynein arms (ODAs) on the axonemal doublet microtubules (DMTs) in cilia and flagella. The docking complex is hypothesized to ...The docking complex is a molecular complex necessary for assembly of outer dynein arms (ODAs) on the axonemal doublet microtubules (DMTs) in cilia and flagella. The docking complex is hypothesized to be a 24-nm molecular ruler because ODAs align along the DMTs with 24-nm periodicity. In this study, we rigorously tested this hypothesis using structural and genetic methods. We found that the ODAs can bind to DMTs and porcine microtubules with 24-nm periodicities even in the absence of the docking complexin vitro Using cryo-electron tomography and structural labeling, we observed that the docking complex took an unexpectedly flexible conformation and did not lie along the length of DMTs. In the absence of docking complex, ODAs were released from the DMT at relatively low ionic strength conditions, suggesting that the docking complex strengthens the electrostatic interactions between the ODA and DMT. Based on these results, we conclude that the docking complex serves as a flexible stabilizer of the ODA rather than as a molecular ruler.
History
DepositionNov 12, 2015-
Header (metadata) releaseNov 25, 2015-
Map releaseMar 16, 2016-
UpdateMar 16, 2016-
Current statusMar 16, 2016Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 27.7
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 27.7
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

400_6510.gif

Downloads & links

-
Map

FileDownload / File: emd_6510.map.gz / Format: CCP4 / Size: 1.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStreptavidin-labeled DC2-M412BCCP axoneme
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
6.07 Å/pix.
x 70 pix.
= 424.9 Å		6.07 Å/pix.
x 70 pix.
= 424.9 Å		6.07 Å/pix.
x 70 pix.
= 424.9 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 6.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 27.699999999999999 / Movie #1: 27.7
Minimum - Maximum-162.394134519999994 - 284.462463379999974
Average (Standard dev.)16.329233169999998 (±70.998786929999994)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions707070
Spacing707070
CellA=B=C: 424.90002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z6.076.076.07
M x/y/z707070
origin x/y/z0.0000.0000.000
length x/y/z424.900424.900424.900
α/β/γ90.00090.00090.000
start NX/NY/NZ-300-64
NX/NY/NZ6161129
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS707070
D min/max/mean-162.394284.46216.329

-
Supplemental data

-
Sample components

-
Entire : Streptavidin-labeled ODA structure from DC2-M412BCCP axoneme

EntireName: Streptavidin-labeled ODA structure from DC2-M412BCCP axoneme
Components
  • Sample: Streptavidin-labeled ODA structure from DC2-M412BCCP axoneme
  • Organelle or cellular component: axoneme

-
Supramolecule #1000: Streptavidin-labeled ODA structure from DC2-M412BCCP axoneme

SupramoleculeName: Streptavidin-labeled ODA structure from DC2-M412BCCP axoneme
type: sample / ID: 1000 / Number unique components: 1

-
Supramolecule #1: axoneme

SupramoleculeName: axoneme / type: organelle_or_cellular_component / ID: 1 / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Chlamydomonas reinhardtii (plant) / Organelle: flagella

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

-
Sample preparation

Concentration0.01 mg/mL
BufferpH: 7.2
Details: 30 mM Hepes-NaOH pH 7.2, 5 mM MgCl2, 1 mM dithiothreitol, 1 mM EGTA, 50 mM K-acetate
GridDetails: 300 mesh copper grid, holey carbon
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 93 K / Instrument: LEICA EM GP / Method: Blot for 5 seconds before plunging

-
Electron microscopy

MicroscopeOTHER
Specialist opticsEnergy filter - Name: Omega / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV
DateFeb 20, 2015
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Average electron dose: 100 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm / Nominal defocus max: 9.0 µm / Nominal defocus min: 6.0 µm / Nominal magnification: 25700
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN / Tilt series - Axis1 - Min angle: -60 ° / Tilt series - Axis1 - Max angle: 60 °

-
Image processing

DetailsNumber of tilts (projections) used in 3D reconstruction: 60 Tomographic tilt angle increment: 2
Final reconstructionResolution.type: BY AUTHOR / Resolution: 47.0 Å / Resolution method: OTHER / Software - Name: IMOD, PEET / Number subtomograms used: 936

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
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.
  • 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 Accession Codes are Changing Soon! / 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.
  • 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

-
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.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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