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- EMDB-4304: Cryo-EM subtomogram average of IFT complex A in anterograde IFT t... -

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Basic information

Entry
Database: EMDB / ID: EMD-4304
TitleCryo-EM subtomogram average of IFT complex A in anterograde IFT trains (Chlamydomonas reinhardtii)
Map dataCryo-EM subtomogram average of IFT complex A in anterograde IFT trains (Chlamydomonas reinhartdii)
Sample
  • Complex: Intraflagellar transport complex A
Function / homology
Function and homology information


negative regulation of eating behavior / protein localization to non-motile cilium / smoothened signaling pathway involved in dorsal/ventral neural tube patterning / myotome development / regulation of intraciliary retrograde transport / forebrain dorsal/ventral pattern formation / ear morphogenesis / intraciliary anterograde transport / cone photoreceptor outer segment / digestive system development ...negative regulation of eating behavior / protein localization to non-motile cilium / smoothened signaling pathway involved in dorsal/ventral neural tube patterning / myotome development / regulation of intraciliary retrograde transport / forebrain dorsal/ventral pattern formation / ear morphogenesis / intraciliary anterograde transport / cone photoreceptor outer segment / digestive system development / intraciliary transport particle A / embryonic heart tube left/right pattern formation / embryonic body morphogenesis / photoreceptor cell outer segment organization / neural tube patterning / protein localization to ciliary membrane / cerebellar Purkinje cell differentiation / intraciliary retrograde transport / embryonic camera-type eye development / establishment of protein localization to organelle / gonad development / intraciliary transport / spinal cord dorsal/ventral patterning / regulation of cilium assembly / photoreceptor connecting cilium / ciliary tip / ventricular system development / Intraflagellar transport / camera-type eye morphogenesis / embryonic brain development / protein localization to cilium / non-motile cilium assembly / regulation of smoothened signaling pathway / embryonic heart tube development / embryonic cranial skeleton morphogenesis / non-motile cilium / embryonic forelimb morphogenesis / nervous system process / determination of left/right symmetry / embryonic limb morphogenesis / limb development / motile cilium / embryonic digit morphogenesis / smoothened signaling pathway / receptor clustering / Bergmann glial cell differentiation / centriolar satellite / axoneme / cilium assembly / photoreceptor outer segment / Hedgehog 'off' state / negative regulation of smoothened signaling pathway / centriole / cellular response to leukemia inhibitory factor / ciliary basal body / neural tube closure / cell morphogenesis / cilium / microtubule cytoskeleton / positive regulation of canonical Wnt signaling pathway / heart development / protein-containing complex assembly / in utero embryonic development / cytoskeleton / intracellular signal transduction / centrosome / positive regulation of gene expression / chromatin binding / regulation of transcription by RNA polymerase II / membrane / plasma membrane / cytoplasm
Similarity search - Function
Intraflagellar transport protein 43 / Intraflagellar transport protein 43 / Tetratricopeptide repeat protein 21A/21B / WD repeat protein 35 / WDR19, WD40 repeat / WD repeat-containing protein 19/dyf-2 / WDR19 second beta-propeller / Intraflagellar transport protein 122 homolog / Tetratricopeptide repeat / Tetratricopeptide repeat ...Intraflagellar transport protein 43 / Intraflagellar transport protein 43 / Tetratricopeptide repeat protein 21A/21B / WD repeat protein 35 / WDR19, WD40 repeat / WD repeat-containing protein 19/dyf-2 / WDR19 second beta-propeller / Intraflagellar transport protein 122 homolog / Tetratricopeptide repeat / Tetratricopeptide repeat / Anaphase-promoting complex subunit 4, WD40 domain / Anaphase-promoting complex subunit 4 WD40 domain / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Tetratricopeptide repeat protein 21B / WD repeat-containing protein 19 / Intraflagellar transport protein 43 homolog / Intraflagellar transport protein 140 homolog / Intraflagellar transport protein 122 homolog / WD repeat-containing protein 35
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
Methodsubtomogram averaging / cryo EM / Resolution: 33.0 Å
AuthorsPigino G / Jordan MA
CitationJournal: Nat Cell Biol / Year: 2018
Title: The cryo-EM structure of intraflagellar transport trains reveals how dynein is inactivated to ensure unidirectional anterograde movement in cilia.
Authors: Mareike A Jordan / Dennis R Diener / Ludek Stepanek / Gaia Pigino /
Abstract: Movement of cargos along microtubules plays key roles in diverse cellular processes, from signalling to mitosis. In cilia, rapid movement of ciliary components along the microtubules to and from the ...Movement of cargos along microtubules plays key roles in diverse cellular processes, from signalling to mitosis. In cilia, rapid movement of ciliary components along the microtubules to and from the assembly site is essential for the assembly and disassembly of the structure itself. This bidirectional transport, known as intraflagellar transport (IFT), is driven by the anterograde motor kinesin-2 and the retrograde motor dynein-1b (dynein-2 in mammals). However, to drive retrograde transport, dynein-1b must first be delivered to the ciliary tip by anterograde IFT. Although, the presence of opposing motors in bidirectional transport processes often leads to periodic stalling and slowing of cargos, IFT is highly processive. Using cryo-electron tomography, we show that a tug-of-war between kinesin-2 and dynein-1b is prevented by loading dynein-1b onto anterograde IFT trains in an autoinhibited form and by positioning it away from the microtubule track to prevent binding. Once at the ciliary tip, dynein-1b must transition into an active form and engage microtubules to power retrograde trains. These findings provide a striking example of how coordinated structural changes mediate the behaviour of complex cellular machinery.
History
DepositionFeb 21, 2018-
Header (metadata) releaseMar 28, 2018-
Map releaseOct 31, 2018-
UpdateNov 7, 2018-
Current statusNov 7, 2018Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.512
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.512
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4304_1.png

emd_4304_2.png

emd_4304_3.png

Downloads & links

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Map

FileDownload / File: emd_4304.map.gz / Format: CCP4 / Size: 48.8 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM subtomogram average of IFT complex A in anterograde IFT trains (Chlamydomonas reinhartdii)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
14.13 Å/pix.
x 33 pix.
= 466.29 Å		14.13 Å/pix.
x 17 pix.
= 240.21 Å		14.13 Å/pix.
x 22 pix.
= 310.86 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 14.13 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.512 / Movie #1: 0.512
Minimum - Maximum-2.6606517 - 2.8285213
Average (Standard dev.)0.0071905465 (±0.53182364)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-10-8-7
Dimensions172233
Spacing221733
CellA: 310.86002 Å / B: 240.21 Å / C: 466.29 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z14.1314.1314.13
M x/y/z221733
origin x/y/z0.0000.0000.000
length x/y/z310.860240.210466.290
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ240240240
MAP C/R/S123
start NC/NR/NS-8-10-7
NC/NR/NS221733
D min/max/mean-2.6612.8290.007

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Supplemental data

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Sample components

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Entire : Intraflagellar transport complex A

EntireName: Intraflagellar transport complex A
Components
  • Complex: Intraflagellar transport complex A

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Supramolecule #1: Intraflagellar transport complex A

SupramoleculeName: Intraflagellar transport complex A / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Chlamydomonas reinhardtii (plant) / Strain: CC-124

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation state2D array

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Sample preparation

BufferpH: 7
GridModel: Quantifoil R3.5/1 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TITAN
Specialist opticsEnergy filter - Name: GIF Quantum LS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 2.1 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: 33.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: PEET (ver. 1.11.0) / Number subtomograms used: 1450
ExtractionNumber tomograms: 15 / Number images used: 750
CTF correctionSoftware - Name: CTFPHASEFLIP
Final angle assignmentType: NOT APPLICABLE

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