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- EMDB-19518: IFTB1 (proximal region) in retrograde Intraflagellar transport trains -

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Basic information

Entry
Database: EMDB / ID: EMD-19518
TitleIFTB1 (proximal region) in retrograde Intraflagellar transport trains
Map dataOverall unfiltered map
Sample
  • Cell: In situ retrograde intraflagellar transport trains in dhc1b-3 mutant Chlamydomonas reinhardtii cilia
KeywordsCilia / IFT / train / retrograde / PROTEIN TRANSPORT
Biological speciesChlamydomonas reinhardtii (plant)
Methodsubtomogram averaging / cryo EM / Resolution: 18.05 Å
AuthorsLacey SE / Pigino G
Funding supportEuropean Union, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
Other government
CitationJournal: Cell / Year: 2024
Title: Extensive structural rearrangement of intraflagellar transport trains underpins bidirectional cargo transport.
Authors: Samuel E Lacey / Andrea Graziadei / Gaia Pigino /
Abstract: Bidirectional transport in cilia is carried out by polymers of the IFTA and IFTB protein complexes, called anterograde and retrograde intraflagellar transport (IFT) trains. Anterograde trains deliver ...Bidirectional transport in cilia is carried out by polymers of the IFTA and IFTB protein complexes, called anterograde and retrograde intraflagellar transport (IFT) trains. Anterograde trains deliver cargoes from the cell to the cilium tip, then convert into retrograde trains for cargo export. We set out to understand how the IFT complexes can perform these two directly opposing roles before and after conversion. We use cryoelectron tomography and in situ cross-linking mass spectrometry to determine the structure of retrograde IFT trains and compare it with the known structure of anterograde trains. The retrograde train is a 2-fold symmetric polymer organized around a central thread of IFTA complexes. We conclude that anterograde-to-retrograde remodeling involves global rearrangements of the IFTA/B complexes and requires complete disassembly of the anterograde train. Finally, we describe how conformational changes to cargo-binding sites facilitate unidirectional cargo transport in a bidirectional system.
History
DepositionJan 31, 2024-
Header (metadata) releaseJul 24, 2024-
Map releaseJul 24, 2024-
UpdateAug 6, 2025-
Current statusAug 6, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19518.png

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Map

FileDownload / File: emd_19518.map.gz / Format: CCP4 / Size: 10.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationOverall unfiltered map
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
6.06 Å/pix.
x 140 pix.
= 848.4 Å		6.06 Å/pix.
x 140 pix.
= 848.4 Å		6.06 Å/pix.
x 140 pix.
= 848.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 6.06 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.7210517 - 1.0973276
Average (Standard dev.)-0.010810825 (±0.09010945)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions140140140
Spacing140140140
CellA=B=C: 848.39996 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_19518_msk_1.map
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Additional map: The main map after Locspiral filtering and masking....

Fileemd_19518_additional_1.map
AnnotationThe main map after Locspiral filtering and masking. This was then used for composite map generation
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Half map: #2

Fileemd_19518_half_map_1.map
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Half map: #1

Fileemd_19518_half_map_2.map
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Sample components

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Entire : In situ retrograde intraflagellar transport trains in dhc1b-3 mut...

EntireName: In situ retrograde intraflagellar transport trains in dhc1b-3 mutant Chlamydomonas reinhardtii cilia
Components
  • Cell: In situ retrograde intraflagellar transport trains in dhc1b-3 mutant Chlamydomonas reinhardtii cilia

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Supramolecule #1: In situ retrograde intraflagellar transport trains in dhc1b-3 mut...

SupramoleculeName: In situ retrograde intraflagellar transport trains in dhc1b-3 mutant Chlamydomonas reinhardtii cilia
type: cell / ID: 1 / Parent: 0
Details: Temperature sensitive cells incubated at restrictive temperature (34 degrees C) for 10 hours and plunge frozen on grids.
Source (natural)Organism: Chlamydomonas reinhardtii (plant) / Strain: dhc1b-3

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 2.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 18.05 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.3) / Number subtomograms used: 3177
ExtractionNumber tomograms: 756 / Number images used: 10455
CTF correctionSoftware - Name: CTFFIND (ver. 4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: MAXIMUM LIKELIHOOD

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