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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


regulation of intraciliary retrograde transport / protein localization to non-motile cilium / intraciliary anterograde transport / intraciliary transport particle A / embryonic body morphogenesis / embryonic heart tube left/right pattern formation / protein localization to ciliary membrane / spinal cord dorsal/ventral patterning / establishment of protein localization to organelle / intraciliary transport ...regulation of intraciliary retrograde transport / protein localization to non-motile cilium / intraciliary anterograde transport / intraciliary transport particle A / embryonic body morphogenesis / embryonic heart tube left/right pattern formation / protein localization to ciliary membrane / spinal cord dorsal/ventral patterning / establishment of protein localization to organelle / intraciliary transport / intraciliary retrograde transport / regulation of cilium assembly / embryonic forelimb morphogenesis / photoreceptor connecting cilium / embryonic heart tube development / camera-type eye morphogenesis / ciliary transition zone / Intraflagellar transport / protein localization to cilium / non-motile cilium assembly / non-motile cilium / motile cilium / sperm principal piece / neural tube closure / intercellular bridge / ciliary tip / limb development / photoreceptor outer segment / axoneme / cilium assembly / Hedgehog 'off' state / centriole / negative regulation of smoothened signaling pathway / sperm midpiece / microtubule cytoskeleton / cilium / protein-containing complex assembly / ciliary basal body / intracellular signal transduction / centrosome / chromatin binding / regulation of transcription by RNA polymerase II / membrane
Similarity search - Function
IFT144, first zinc finger domain / Intraflagellar transport protein 43 / Intraflagellar transport protein 43 / IFT122, C-terminal zinc ribbon domain / : / IFT122, zinc ribbon domain / Tetratricopeptide repeat protein 21A/21B / : / : / : ...IFT144, first zinc finger domain / Intraflagellar transport protein 43 / Intraflagellar transport protein 43 / IFT122, C-terminal zinc ribbon domain / : / IFT122, zinc ribbon domain / Tetratricopeptide repeat protein 21A/21B / : / : / : / : / : / Tetratricopeptide repeat protein 21 ARM repeat / Tetratricopeptide repeat protein 21 second ARM domain / Tetratricopeptide repeat protein 21 N-terminal ARM repeat / Tetratricopeptide repeat protein 21 C-terminal ARM domain / TT21 fifth ARM repeats domain / Tetratricopeptide repeat protein 21 forth ARM domain / WD repeat protein 35 / WDR19, WD40 repeat / WD repeat-containing protein 19/dyf-2 / : / : / : / : / : / : / : / : / WDR19 second beta-propeller / IFT140 first beta-propeller / IFT140 second beta-propeller / WDR19 first beta-propeller / WDR35 second beta-propeller / IF140 C-terminal TPR domain / WDR35/TULP4 N-terminal / WD repeat-containing protein 35, TPR repeats / IFT121-like, TPR repeats / : / : / IFT121, second zinc finger domain / IF140/IFT172 TPR domain / : / IFT80/172/WDR35/WDR19 TPR domain / Intraflagellar transport protein 122 homolog / : / : / IFT122 second beta-propeller / IFT122, TPR domain / : / IFT122 first beta-propeller / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / 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
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  • 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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