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- EMDB-16310: In situ outer dynein arm from Chlamydomonas reinhardtii in an int... -

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Basic information

Entry
Database: EMDB / ID: EMD-16310
TitleIn situ outer dynein arm from Chlamydomonas reinhardtii in an intermediate
Map data
Sample
  • Organelle or cellular component: In situ outer dynein arm
Keywordsaxoneme / outer dynein arm / power stroke / dynein / MOTOR PROTEIN
Biological speciesChlamydomonas reinhardtii (plant)
Methodsubtomogram averaging / cryo EM / Resolution: 37.7 Å
AuthorsZimmermann NEL / Noga A / Obbineni JM / Ishikawa T
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science FoundationNF310030_192644 Switzerland
CitationJournal: EMBO J / Year: 2023
Title: ATP-induced conformational change of axonemal outer dynein arms revealed by cryo-electron tomography.
Authors: Noemi Zimmermann / Akira Noga / Jagan Mohan Obbineni / Takashi Ishikawa /
Abstract: Axonemal outer dynein arm (ODA) motors generate force for ciliary beating. We analyzed three states of the ODA during the power stroke cycle using in situ cryo-electron tomography, subtomogram ...Axonemal outer dynein arm (ODA) motors generate force for ciliary beating. We analyzed three states of the ODA during the power stroke cycle using in situ cryo-electron tomography, subtomogram averaging, and classification. These states of force generation depict the prepower stroke, postpower stroke, and intermediate state conformations. Comparison of these conformations to published in vitro atomic structures of cytoplasmic dynein, ODA, and the Shulin-ODA complex revealed differences in the orientation and position of the dynein head. Our analysis shows that in the absence of ATP, all dynein linkers interact with the AAA3/AAA4 domains, indicating that interactions with the adjacent microtubule doublet B-tubule direct dynein orientation. For the prepower stroke conformation, there were changes in the tail that is anchored on the A-tubule. We built models starting with available high-resolution structures to generate a best-fitting model structure for the in situ pre- and postpower stroke ODA conformations, thereby showing that ODA in a complex with Shulin adopts a similar conformation as the active prepower stroke ODA in the axoneme.
History
DepositionDec 8, 2022-
Header (metadata) releaseApr 26, 2023-
Map releaseApr 26, 2023-
UpdateJun 28, 2023-
Current statusJun 28, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16310.png

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Map

FileDownload / File: emd_16310.map.gz / Format: CCP4 / Size: 1.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
8.5 Å/pix.
x 74 pix.
= 629. Å		8.5 Å/pix.
x 74 pix.
= 629. Å		8.5 Å/pix.
x 74 pix.
= 629. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 8.5 Å
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Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.22781362 - 0.3149952
Average (Standard dev.)0.003423612 (±0.0555474)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions747474
Spacing747474
CellA=B=C: 629.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_16310_half_map_1.map
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Half map: #2

Fileemd_16310_half_map_2.map
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Sample components

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Entire : In situ outer dynein arm

EntireName: In situ outer dynein arm
Components
  • Organelle or cellular component: In situ outer dynein arm

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Supramolecule #1: In situ outer dynein arm

SupramoleculeName: In situ outer dynein arm / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#21
Source (natural)Organism: Chlamydomonas reinhardtii (plant)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 5.0 µm / Nominal defocus min: 4.0 µm
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 1.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

ExtractionNumber tomograms: 12 / Number images used: 3553
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 37.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 256

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT

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