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- EMDB-11577: Outer Dynein Arm-Shulin complex - full tail region (Tetrahymena t... -

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Basic information

Entry
Database: EMDB / ID: EMD-11577
TitleOuter Dynein Arm-Shulin complex - full tail region (Tetrahymena thermophila)
Map dataMain map of full ODA-Shulin tail (resampled on full-length ODA-Shulin structure using EMDA). Unsharpened map.
Sample
  • Complex: Tetrahymena thermophila ODA Dyh4 motor
Biological speciesTetrahymena thermophila (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.66 Å
AuthorsMali GR / Abid Ali F / Lau CK / Begum F / Boulanger J / Howe JD / Chen ZA / Rappsilber J / Skehel M / 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: 0.002
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.002
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_11577.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map of full ODA-Shulin tail (resampled on full-length ODA-Shulin structure using EMDA). Unsharpened map.
Voxel sizeX=Y=Z: 1.11 Å
Density
Contour LevelBy AUTHOR: 0.002 / Movie #1: 0.002
Minimum - Maximum-0.008801127 - 0.013784549
Average (Standard dev.)2.695596e-06 (±0.00055499224)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 499.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.111.111.11
M x/y/z450450450
origin x/y/z0.0000.0000.000
length x/y/z499.500499.500499.500
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS450450450
D min/max/mean-0.0090.0140.000

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Supplemental data

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Mask #1

Fileemd_11577_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: Mask for full ODA-Shulin tail (Z-flipped, non resampled)...

Fileemd_11577_additional_1.map
AnnotationMask for full ODA-Shulin tail (Z-flipped, non resampled) to be used with half maps.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Half map 2 of full ODA-Shulin tail (Z-flipped, non-resampled)

Fileemd_11577_half_map_1.map
AnnotationHalf map 2 of full ODA-Shulin tail (Z-flipped, non-resampled)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: Half map 1 of full ODA-Shulin tail (Z-flipped, non-resampled)

Fileemd_11577_half_map_2.map
AnnotationHalf map 1 of full ODA-Shulin tail (Z-flipped, non-resampled)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire : Tetrahymena thermophila ODA Dyh4 motor

EntireName: Tetrahymena thermophila ODA Dyh4 motor
Components
  • Complex: Tetrahymena thermophila ODA Dyh4 motor

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Supramolecule #1: Tetrahymena thermophila ODA Dyh4 motor

SupramoleculeName: Tetrahymena thermophila ODA Dyh4 motor / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Tetrahymena thermophila (eukaryote)
Molecular weightTheoretical: 1.8 MDa

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

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationSoftware - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.66 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 131142
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT

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