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- EMDB-11583: Outer Dynein Arm-Shulin complex - Dyh5 motor (Tetrahymena thermophila) -

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Basic information

Entry
Database: EMDB / ID: EMD-11583
TitleOuter Dynein Arm-Shulin complex - Dyh5 motor (Tetrahymena thermophila)
Map dataMain map of Dyh5 motor (resampled on a full-length ODA-Shulin structure from a smaller subset of particles using EMDA). -148 angstrom auto-sharpened map.
Sample
  • Complex: Tetrahymena thermophila ODA Dyh5 motor
Biological speciesTetrahymena thermophila (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.62 Å
AuthorsMali GR / Abid Ali F / Lau CK / Carter AP
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
Medical Research Council (MRC, United Kingdom) United Kingdom
CitationJournal: Science / Year: 2021
Title: Shulin packages axonemal outer dynein arms for ciliary targeting.
Authors: Girish R Mali / Ferdos Abid Ali / Clinton K Lau / Farida Begum / Jérôme Boulanger / Jonathan D Howe / Zhuo A Chen / Juri Rappsilber / Mark Skehel / Andrew P Carter /
Abstract: The main force generators in eukaryotic cilia and flagella are axonemal outer dynein arms (ODAs). During ciliogenesis, these ~1.8-megadalton complexes are assembled in the cytoplasm and targeted to ...The main force generators in eukaryotic cilia and flagella are axonemal outer dynein arms (ODAs). During ciliogenesis, these ~1.8-megadalton complexes are assembled in the cytoplasm and targeted to cilia by an unknown mechanism. Here, we used the ciliate to identify two factors (Q22YU3 and Q22MS1) that bind ODAs in the cytoplasm and are required for ODA delivery to cilia. Q22YU3, which we named Shulin, locked the ODA motor domains into a closed conformation and inhibited motor activity. Cryo-electron microscopy revealed how Shulin stabilized this compact form of ODAs by binding to the dynein tails. Our findings provide a molecular explanation for how newly assembled dyneins are packaged for delivery to the cilia.
History
DepositionAug 3, 2020-
Header (metadata) releaseJan 20, 2021-
Map releaseJan 20, 2021-
UpdateMar 17, 2021-
Current statusMar 17, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.014
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.014
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11583.png

Downloads & links

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Map

FileDownload / File: emd_11583.map.gz / Format: CCP4 / Size: 43.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map of Dyh5 motor (resampled on a full-length ODA-Shulin structure from a smaller subset of particles using EMDA). -148 angstrom auto-sharpened map.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.23 Å/pix.
x 225 pix.
= 501.73 Å		2.23 Å/pix.
x 225 pix.
= 501.73 Å		2.23 Å/pix.
x 225 pix.
= 501.73 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.22991 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.014 / Movie #1: 0.014
Minimum - Maximum-0.044965133 - 0.087245196
Average (Standard dev.)-3.5986912e-05 (±0.001968833)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions225225225
Spacing225225225
CellA=B=C: 501.7299 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.22991111111112.22991111111112.2299111111111
M x/y/z225225225
origin x/y/z0.0000.0000.000
length x/y/z501.730501.730501.730
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS225225225
D min/max/mean-0.0450.087-0.000

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Supplemental data

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Mask #1

Fileemd_11583_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Mask for Dyh5 motor map (Z-flipped, non resampled)...

Fileemd_11583_additional_1.map
AnnotationMask for Dyh5 motor map (Z-flipped, non resampled) to be used with half maps.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1 of Dyh5 motor map (Z-flipped, non-resampled)

Fileemd_11583_half_map_1.map
AnnotationHalf map 1 of Dyh5 motor map (Z-flipped, non-resampled)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2 of Dyh5 motor map (Z-flipped, non-resampled)

Fileemd_11583_half_map_2.map
AnnotationHalf map 2 of Dyh5 motor map (Z-flipped, non-resampled)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Tetrahymena thermophila ODA Dyh5 motor

EntireName: Tetrahymena thermophila ODA Dyh5 motor
Components
  • Complex: Tetrahymena thermophila ODA Dyh5 motor

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Supramolecule #1: Tetrahymena thermophila ODA Dyh5 motor

SupramoleculeName: Tetrahymena thermophila ODA Dyh5 motor / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Tetrahymena thermophila (eukaryote)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.2 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R2/2 / Material: GOLD / Support film - Material: GRAPHENE OXIDE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.62 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 49756
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationSoftware - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT

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