[English] 日本語
Yorodumi
- EMDB-20341: The Nexin-dynein Regulatory Complex (N-DRC) from the cryo-electro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-20341
TitleThe Nexin-dynein Regulatory Complex (N-DRC) from the cryo-electron tomography and subtomographic average of isolated Chlamydomonas SNAP-DRC4 axonemes, labeled with streptavidin-nanogold
Map dataN-DRC structure from SNAP-DRC4 Chlamydomonas
Sample
  • Cell: The nexin-dynein regulatory complex averaged from Chlamydomonas SNAP-DRC4 axoneme, labeled with streptavidin-nanogold
Biological speciesChlamydomonas reinhardtii (plant)
Methodsubtomogram averaging / cryo EM / Resolution: 35.0 Å
AuthorsGui L / Song K / Tritschler D / Bower R / Yan S / Dai A / Augspurger K / Sakizadeh J / Grzemska M / Ni T ...Gui L / Song K / Tritschler D / Bower R / Yan S / Dai A / Augspurger K / Sakizadeh J / Grzemska M / Ni T / Porter ME / Nicastro D
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical SciencesR01GM083122 United States
National Institutes of Health/National Institute of General Medical SciencesR01GM055667 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2019
Title: Scaffold subunits support associated subunit assembly in the ciliary nexin-dynein regulatory complex.
Authors: Long Gui / Kangkang Song / Douglas Tritschler / Raqual Bower / Si Yan / Aguang Dai / Katherine Augspurger / Jason Sakizadeh / Magdalena Grzemska / Thomas Ni / Mary E Porter / Daniela Nicastro /
Abstract: The nexin-dynein regulatory complex (N-DRC) in motile cilia and flagella functions as a linker between neighboring doublet microtubules, acts to stabilize the axonemal core structure, and serves as a ...The nexin-dynein regulatory complex (N-DRC) in motile cilia and flagella functions as a linker between neighboring doublet microtubules, acts to stabilize the axonemal core structure, and serves as a central hub for the regulation of ciliary motility. Although the N-DRC has been studied extensively using genetic, biochemical, and structural approaches, the precise arrangement of the 11 (or more) N-DRC subunits remains unknown. Here, using cryo-electron tomography, we have compared the structure of wild-type flagella to that of strains with specific DRC subunit deletions or rescued strains with tagged DRC subunits. Our results show that DRC7 is a central linker subunit that helps connect the N-DRC to the outer dynein arms. DRC11 is required for the assembly of DRC8, and DRC8/11 form a subcomplex in the proximal lobe of the linker domain that is required to form stable contacts to the neighboring B-tubule. Gold labeling of tagged subunits determines the precise locations of the previously ambiguous N terminus of DRC4 and C terminus of DRC5. DRC4 is now shown to contribute to the core scaffold of the N-DRC. Our results reveal the overall architecture of N-DRC, with the 3 subunits DRC1/2/4 forming a core complex that serves as the scaffold for the assembly of the "functional subunits," namely DRC3/5-8/11. These findings shed light on N-DRC assembly and its role in regulating flagellar beating.
History
DepositionJun 25, 2019-
Header (metadata) releaseJul 24, 2019-
Map releaseNov 6, 2019-
UpdateNov 27, 2019-
Current statusNov 27, 2019Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 132
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 132
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20341.png

Downloads & links

-
Map

FileDownload / File: emd_20341.map.gz / Format: CCP4 / Size: 548.8 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationN-DRC structure from SNAP-DRC4 Chlamydomonas
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
10.77 Å/pix.
x 65 pix.
= 700.282 Å		10.77 Å/pix.
x 40 pix.
= 430.943 Å		10.77 Å/pix.
x 54 pix.
= 581.772 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 10.77356 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 132 / Movie #1: 132
Minimum - Maximum101.08708 - 167.4963
Average (Standard dev.)128.44873 (±10.965531)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-40-47-36
Dimensions405465
Spacing544065
CellA: 581.77246 Å / B: 430.94257 Å / C: 700.2817 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z10.77355555555610.77357510.773569230769
M x/y/z544065
origin x/y/z0.0000.0000.000
length x/y/z581.772430.943700.282
α/β/γ90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS-47-40-36
NC/NR/NS544065
D min/max/mean101.087167.496128.449

-
Supplemental data

-
Sample components

-
Entire : The nexin-dynein regulatory complex averaged from Chlamydomonas S...

EntireName: The nexin-dynein regulatory complex averaged from Chlamydomonas SNAP-DRC4 axoneme, labeled with streptavidin-nanogold
Components
  • Cell: The nexin-dynein regulatory complex averaged from Chlamydomonas SNAP-DRC4 axoneme, labeled with streptavidin-nanogold

-
Supramolecule #1: The nexin-dynein regulatory complex averaged from Chlamydomonas S...

SupramoleculeName: The nexin-dynein regulatory complex averaged from Chlamydomonas SNAP-DRC4 axoneme, labeled with streptavidin-nanogold
type: cell / ID: 1 / Parent: 0
Details: Axonemes from the N-terminal SNAP tagged DRC4 rescued Chlamydomonas pf2-4 strain, labeled with streptavidin-nanogold
Source (natural)Organism: Chlamydomonas reinhardtii (plant) / Strain: pf2-4

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

-
Sample preparation

BufferpH: 7.4
GridDetails: unspecified
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TECNAI F30
Image recordingFilm or detector model: GATAN ULTRASCAN 1000 (2k x 2k) / Average electron dose: 1.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

-
Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 35.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number subtomograms used: 973
ExtractionNumber tomograms: 9 / Number images used: 973
Final angle assignmentType: OTHER

+
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