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- EMDB-20341: The Nexin-dynein Regulatory Complex (N-DRC) from the cryo-electro... -

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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

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Structure visualization

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

emd_20341.png

Downloads & links

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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
Voxel sizeX=Y=Z: 10.77356 Å
Density
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

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Supplemental data

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Sample components

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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

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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

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7.4
GridDetails: unspecified
VitrificationCryogen name: ETHANE

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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

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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

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