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Yorodumi- EMDB-4304: Cryo-EM subtomogram average of IFT complex A in anterograde IFT t... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4304 | |||||||||
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Title | Cryo-EM subtomogram average of IFT complex A in anterograde IFT trains (Chlamydomonas reinhardtii) | |||||||||
Map data | Cryo-EM subtomogram average of IFT complex A in anterograde IFT trains (Chlamydomonas reinhartdii) | |||||||||
Sample |
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Function / homology | Function and homology information smoothened signaling pathway involved in dorsal/ventral neural tube patterning / myotome development / protein localization to non-motile cilium / regulation of intraciliary retrograde transport / : / forebrain dorsal/ventral pattern formation / ear morphogenesis / intraciliary transport particle A / intraciliary anterograde transport / cone photoreceptor outer segment ...smoothened signaling pathway involved in dorsal/ventral neural tube patterning / myotome development / protein localization to non-motile cilium / regulation of intraciliary retrograde transport / : / forebrain dorsal/ventral pattern formation / ear morphogenesis / intraciliary transport particle A / intraciliary anterograde transport / cone photoreceptor outer segment / negative regulation of eating behavior / digestive system development / embryonic heart tube left/right pattern formation / embryonic body morphogenesis / photoreceptor cell outer segment organization / neural tube patterning / intraciliary retrograde transport / protein localization to ciliary membrane / cerebellar Purkinje cell differentiation / intraciliary transport / establishment of protein localization to organelle / embryonic camera-type eye development / gonad development / regulation of cilium assembly / spinal cord dorsal/ventral patterning / 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 / non-motile cilium / embryonic heart tube development / regulation of smoothened signaling pathway / embryonic cranial skeleton morphogenesis / nervous system process / motile cilium / embryonic forelimb morphogenesis / determination of left/right symmetry / embryonic limb morphogenesis / limb development / smoothened signaling pathway / embryonic digit morphogenesis / receptor clustering / axoneme / Bergmann glial cell differentiation / centriolar satellite / 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 / positive regulation of canonical Wnt signaling pathway / microtubule cytoskeleton / heart development / protein-containing complex assembly / in utero embryonic development / cytoskeleton / centrosome / chromatin binding / positive regulation of gene expression / regulation of transcription by RNA polymerase II / membrane / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Chlamydomonas reinhardtii (plant) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 33.0 Å | |||||||||
Authors | Pigino G / Jordan MA | |||||||||
Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4304.map.gz | 30.1 KB | EMDB map data format | |
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Header (meta data) | emd-4304-v30.xml emd-4304.xml | 8.4 KB 8.4 KB | Display Display | EMDB header |
Images | emd_4304_1.png emd_4304_2.png emd_4304_3.png | 142.5 KB 95.8 KB 85.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4304 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4304 | HTTPS FTP |
-Related structure data
Related structure data | 8bbgM 4303C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_4304.map.gz / Format: CCP4 / Size: 48.8 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM subtomogram average of IFT complex A in anterograde IFT trains (Chlamydomonas reinhartdii) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 14.13 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Intraflagellar transport complex A
Entire | Name: Intraflagellar transport complex A |
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Components |
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-Supramolecule #1: Intraflagellar transport complex A
Supramolecule | Name: Intraflagellar transport complex A / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Chlamydomonas reinhardtii (plant) / Strain: CC-124 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | 2D array |
-Sample preparation
Buffer | pH: 7 |
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Grid | Model: Quantifoil R3.5/1 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Instrument: LEICA EM GP |
-Electron microscopy
Microscope | FEI TITAN |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Specialist optics | Energy filter - Name: GIF Quantum LS |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 2.1 e/Å2 |
-Image processing
Extraction | Number tomograms: 15 / Number images used: 750 |
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CTF correction | Software - Name: CTFPHASEFLIP |
Final angle assignment | Type: NOT APPLICABLE |
Final reconstruction | Resolution.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 |