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Yorodumi- EMDB-4303: Cryo-EM subtomogram average of IFT complex B and inhibited dynein... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4303 | |||||||||
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Title | Cryo-EM subtomogram average of IFT complex B and inhibited dynein-1b in anterograde IFT trains (Chlamydomonas reinhardtii) | |||||||||
Map data | Cryo-EM stubtomogram average of IFT complex B and inhibited dynein-1b in anterograde IFT trains (Chlamydomonas reinhardtii) | |||||||||
Sample |
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Function / homology | Function and homology information intraciliary transport involved in cilium assembly / positive regulation of non-motile cilium assembly / intraciliary retrograde transport / visual behavior / methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity / ciliary transition zone / dynein light chain binding / intraciliary transport / mitocytosis ...intraciliary transport involved in cilium assembly / positive regulation of non-motile cilium assembly / intraciliary retrograde transport / visual behavior / methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity / ciliary transition zone / dynein light chain binding / intraciliary transport / mitocytosis / motile cilium assembly / dynein heavy chain binding / regulation of cilium assembly / embryonic skeletal system morphogenesis / Activation of BIM and translocation to mitochondria / ciliary tip / DNA modification / Intraflagellar transport / negative regulation of nitric oxide biosynthetic process / negative regulation of phosphorylation / dynein complex / COPI-independent Golgi-to-ER retrograde traffic / minus-end-directed microtubule motor activity / cytoplasmic dynein complex / dynein light intermediate chain binding / ciliary plasm / enzyme inhibitor activity / motile cilium / determination of left/right symmetry / microtubule motor activity / ciliary base / Macroautophagy / dynein intermediate chain binding / microtubule-based movement / pericentriolar material / spermatid development / axoneme / positive regulation of insulin secretion involved in cellular response to glucose stimulus / tertiary granule membrane / ficolin-1-rich granule membrane / cilium assembly / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / COPI-mediated anterograde transport / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / axon cytoplasm / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Resolution of Sister Chromatid Cohesion / Recruitment of NuMA to mitotic centrosomes / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Anchoring of the basal body to the plasma membrane / substantia nigra development / MHC class II antigen presentation / centriole / nitric-oxide synthase regulator activity / AURKA Activation by TPX2 / regulation of mitochondrial membrane potential / ciliary basal body / filopodium / RHO GTPases Activate Formins / cilium / kinetochore / Aggrephagy / HCMV Early Events / mitotic spindle / Separation of Sister Chromatids / Regulation of PLK1 Activity at G2/M Transition / apical part of cell / methylation / scaffold protein binding / microtubule / cytoskeleton / protein domain specific binding / DNA repair / centrosome / apoptotic process / Neutrophil degranulation / protein-containing complex binding / Golgi apparatus / enzyme binding / ATP hydrolysis activity / mitochondrion / extracellular space / ATP binding / membrane / metal ion binding / nucleus / identical protein binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Chlamydomonas reinhardtii (plant) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 37.0 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_4303.map.gz | 168.2 KB | EMDB map data format | |
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Header (meta data) | emd-4303-v30.xml emd-4303.xml | 8.9 KB 8.9 KB | Display Display | EMDB header |
Images | emd_4303_1.png emd_4303_2.png | 284.4 KB 188 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4303 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4303 | HTTPS FTP |
-Related structure data
Related structure data | 6sc2M 4304C 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_4303.map.gz / Format: CCP4 / Size: 306.6 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM stubtomogram average of IFT complex B and inhibited dynein-1b in anterograde IFT trains (Chlamydomonas reinhardtii) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 B and inhibited dynein-1b
Entire | Name: Intraflagellar transport complex B and inhibited dynein-1b |
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Components |
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-Supramolecule #1: Intraflagellar transport complex B and inhibited dynein-1b
Supramolecule | Name: Intraflagellar transport complex B and inhibited dynein-1b 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 / Software - Name: IMOD (ver. 4.9.2) |
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CTF correction | Software - Name: CTFPHASEFLIP |
Final angle assignment | Type: NOT APPLICABLE |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 37.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: PEET (ver. 1.11.0) / Number subtomograms used: 750 |