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- EMDB-47381: Full-length human dynein-1 in phi comformation under Lis1 condition -
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Open data
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Basic information
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Title | Full-length human dynein-1 in phi comformation under Lis1 condition | |||||||||
![]() | Full-length human dynein-1 in phi comformation under Lis1 condition | |||||||||
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![]() | Dynein-1 / phi conformation / MOTOR PROTEIN | |||||||||
Function / homology | ![]() intracellular transport of viral protein in host cell / secretory vesicle / nitric-oxide synthase inhibitor activity / deoxyribonuclease inhibitor activity / negative regulation of DNA strand resection involved in replication fork processing / negative regulation of phosphorylation / transport along microtubule / intraciliary retrograde transport / visual behavior / dynein light chain binding ...intracellular transport of viral protein in host cell / secretory vesicle / nitric-oxide synthase inhibitor activity / deoxyribonuclease inhibitor activity / negative regulation of DNA strand resection involved in replication fork processing / negative regulation of phosphorylation / transport along microtubule / intraciliary retrograde transport / visual behavior / dynein light chain binding / dynein heavy chain binding / motile cilium assembly / Activation of BIM and translocation to mitochondria / ciliary tip / Intraflagellar transport / positive regulation of intracellular transport / negative regulation of nitric oxide biosynthetic process / regulation of metaphase plate congression / establishment of spindle localization / positive regulation of spindle assembly / regulation of G protein-coupled receptor signaling pathway / microtubule-dependent intracellular transport of viral material towards nucleus / dynein complex / COPI-independent Golgi-to-ER retrograde traffic / retrograde axonal transport / minus-end-directed microtubule motor activity / microtubule motor activity / P-body assembly / dynein light intermediate chain binding / cytoplasmic dynein complex / centrosome localization / microtubule-based movement / nuclear migration / Macroautophagy / dynein intermediate chain binding / establishment of mitotic spindle orientation / tertiary granule membrane / ficolin-1-rich granule membrane / enzyme inhibitor activity / spermatid development / positive regulation of insulin secretion involved in cellular response to glucose stimulus / cytoplasmic microtubule / COPI-mediated anterograde transport / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / cytoplasmic microtubule organization / axon cytoplasm / substantia nigra development / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / stress granule assembly / MHC class II antigen presentation / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / regulation of mitotic spindle organization / Resolution of Sister Chromatid Cohesion / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / AURKA Activation by TPX2 / mitotic spindle organization / filopodium / RHO GTPases Activate Formins / cellular response to nerve growth factor stimulus / kinetochore / negative regulation of neurogenesis / Aggrephagy / microtubule cytoskeleton organization / spindle / Separation of Sister Chromatids / HCMV Early Events / Regulation of PLK1 Activity at G2/M Transition / mitotic spindle / azurophil granule lumen / late endosome / site of double-strand break / nervous system development / host cell / positive regulation of cold-induced thermogenesis / scaffold protein binding / cell cortex / vesicle / secretory granule lumen / ficolin-1-rich granule lumen / microtubule / cytoskeleton / cilium / cell division / apoptotic process / centrosome / DNA damage response / Neutrophil degranulation / symbiont entry into host cell / protein-containing complex binding / enzyme binding / Golgi apparatus / ATP hydrolysis activity / mitochondrion / RNA binding / extracellular exosome Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.5 Å | |||||||||
![]() | Yang J / Zhang K | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Nde1 promotes Lis1 binding to full-length autoinhibited human dynein 1. Authors: Jun Yang / Yuanchang Zhao / Pengxin Chai / Ahmet Yildiz / Kai Zhang / ![]() Abstract: Cytoplasmic dynein 1 (dynein) is the primary motor responsible for the retrograde transport of intracellular cargoes along microtubules. Activation of dynein requires the opening its autoinhibited ...Cytoplasmic dynein 1 (dynein) is the primary motor responsible for the retrograde transport of intracellular cargoes along microtubules. Activation of dynein requires the opening its autoinhibited Phi conformation, a process driven by Lis1 and Nde1/Ndel1. Using biochemical reconstitution and cryo-electron microscopy, we demonstrate that Nde1 enhances Lis1 binding to autoinhibited dynein and facilitates Phi opening. We identify a key intermediate in this activation pathway where a single Lis1 dimer binds between Phi-like (Phi) motor rings. In this 'Phi-Lis1' complex, Lis1 interacts with one motor domain through canonical sites at the AAA+ (adenosine triphosphatases associated with diverse cellular activities) ring and stalk, and with AAA5, AAA6 and linker regions of the other motor domain. Mutagenesis and motility assays confirm the critical role of the Phi-Lis1 interface in dynein activation. This intermediate forms rapidly in the presence of Nde1, although Nde1 is not part of Phi-Lis1. These findings provide key insights into how Nde1 promotes Lis1-mediated Phi opening. | |||||||||
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 70.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 24.7 KB 24.7 KB | Display Display | ![]() |
Images | ![]() | 63 KB | ||
Filedesc metadata | ![]() | 10 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 346.7 KB | Display | ![]() |
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Full document | ![]() | 346.3 KB | Display | |
Data in XML | ![]() | 6.9 KB | Display | |
Data in CIF | ![]() | 8.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9e12MC ![]() 9e0zC ![]() 9e10C ![]() 9e11C ![]() 9e13C ![]() 9e14C C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Full-length human dynein-1 in phi comformation under Lis1 condition | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.736 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
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Sample components
+Entire : Full-length human dynein-1 in phi comformation under Lis1 condition
+Supramolecule #1: Full-length human dynein-1 in phi comformation under Lis1 condition
+Macromolecule #1: Cytoplasmic dynein 1 heavy chain 1
+Macromolecule #2: Cytoplasmic dynein 1 intermediate chain 2
+Macromolecule #3: Cytoplasmic dynein 1 light intermediate chain 2
+Macromolecule #4: Dynein light chain roadblock-type 1
+Macromolecule #5: Dynein light chain 1, cytoplasmic
+Macromolecule #6: Dynein light chain Tctex-type 1
+Macromolecule #7: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #8: ADENOSINE-5'-TRIPHOSPHATE
+Macromolecule #9: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 2 mg/mL |
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Buffer | pH: 7.2 |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | TFS GLACIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 30.0 µm / Calibrated defocus max: 2.6 µm / Calibrated defocus min: 1.2 µm / Calibrated magnification: 45000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 45000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |