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- EMDB-19520: IFTB2 in retrograde Intraflagellar transport trains -

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Basic information

Entry
Database: EMDB / ID: EMD-19520
TitleIFTB2 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: 15.4 Å
AuthorsLacey SE / Pigino G
Funding supportEuropean Union, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
Other government
CitationJournal: To Be Published
Title: Retrograde intraflagellar transport trains are a unique polymeric arrangement of IFT complexes
Authors: Lacey SE / Graziadei A / Pigino G
History
DepositionJan 31, 2024-
Header (metadata) releaseJul 24, 2024-
Map releaseJul 24, 2024-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19520.png

Downloads & links

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Map

FileDownload / File: emd_19520.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
Brightness
Contrast
Others
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 6.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.7807842 - 1.4193264
Average (Standard dev.)-0.012427583 (±0.10361535)
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_19520_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: Masked refinement of the region corresponding to IFTA2,...

Fileemd_19520_additional_1.map
AnnotationMasked refinement of the region corresponding to IFTA2, showing the continuation of the IFT81/74 coiled coil to make contact with IFT139
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

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

Fileemd_19520_additional_2.map
AnnotationThe main map after Locspiral filtering and masking. This was then used for composite map generation
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_19520_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_19520_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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
GridModel: Quantifoil R2/2 / Material: GOLD / Pretreatment - Type: PLASMA CLEANING
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: 15.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.3)
Details: Particle number after C2 symmetry expansion of star file
Number subtomograms used: 3891
ExtractionNumber tomograms: 756 / Number images used: 10455
Final angle assignmentType: MAXIMUM LIKELIHOOD

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