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- PDB-9e14: Full-length human dynein-1 in phi-like comformation bound to a Li... -
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Basic information
Entry | Database: PDB / ID: 9.0E+14 | ||||||
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Title | Full-length human dynein-1 in phi-like comformation bound to a Lis1 dimer under Nde1-Lis1 condition | ||||||
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![]() | MOTOR PROTEIN / dynein-1 / phi-like conformation / Lis1 | ||||||
Function / homology | ![]() intracellular transport of viral protein in host cell / corpus callosum morphogenesis / secretory vesicle / nitric-oxide synthase inhibitor activity / microtubule cytoskeleton organization involved in establishment of planar polarity / ameboidal-type cell migration / establishment of planar polarity of embryonic epithelium / 1-alkyl-2-acetylglycerophosphocholine esterase complex / deoxyribonuclease inhibitor activity / negative regulation of DNA strand resection involved in replication fork processing ...intracellular transport of viral protein in host cell / corpus callosum morphogenesis / secretory vesicle / nitric-oxide synthase inhibitor activity / microtubule cytoskeleton organization involved in establishment of planar polarity / ameboidal-type cell migration / establishment of planar polarity of embryonic epithelium / 1-alkyl-2-acetylglycerophosphocholine esterase complex / deoxyribonuclease inhibitor activity / negative regulation of DNA strand resection involved in replication fork processing / maintenance of centrosome location / negative regulation of phosphorylation / platelet activating factor metabolic process / transport along microtubule / intraciliary retrograde transport / visual behavior / radial glia-guided pyramidal neuron migration / acrosome assembly / central region of growth cone / cerebral cortex neuron differentiation / dynein light chain binding / establishment of centrosome localization / microtubule sliding / positive regulation of embryonic development / dynein heavy chain binding / positive regulation of cytokine-mediated signaling pathway / motile cilium assembly / Activation of BIM and translocation to mitochondria / microtubule organizing center organization / interneuron migration / layer formation in cerebral cortex / ciliary tip / auditory receptor cell development / nuclear membrane disassembly / astral microtubule / Intraflagellar transport / positive regulation of dendritic spine morphogenesis / cortical microtubule organization / positive regulation of intracellular transport / negative regulation of nitric oxide biosynthetic process / myeloid leukocyte migration / reelin-mediated signaling pathway / regulation of metaphase plate congression / establishment of spindle localization / positive regulation of spindle assembly / regulation of G protein-coupled receptor signaling pathway / stereocilium / osteoclast development / microtubule plus-end binding / brain morphogenesis / microtubule-dependent intracellular transport of viral material towards nucleus / vesicle transport along microtubule / dynein complex / COPI-independent Golgi-to-ER retrograde traffic / retrograde axonal transport / kinesin complex / minus-end-directed microtubule motor activity / microtubule motor activity / P-body assembly / negative regulation of JNK cascade / microtubule associated complex / dynein light intermediate chain binding / cytoplasmic dynein complex / centrosome localization / motile cilium / neuromuscular process controlling balance / stem cell division / microtubule-based movement / nuclear migration / Macroautophagy / dynein complex binding / cell leading edge / transmission of nerve impulse / dynein intermediate chain binding / germ cell development / establishment of mitotic spindle orientation / dynactin binding / tertiary granule membrane / ficolin-1-rich granule membrane / protein secretion / cochlea development / enzyme inhibitor activity / spermatid development / neuroblast proliferation / positive regulation of insulin secretion involved in cellular response to glucose stimulus / positive regulation of axon extension / microtubule-based process / phospholipase binding / lipid catabolic process / cytoplasmic microtubule / COPI-mediated anterograde transport / JNK cascade / 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 Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 2 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 272.7 KB | Display | |
Data in CIF | ![]() | 429.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 47383MC ![]() 9e0zC ![]() 9e10C ![]() 9e11C ![]() 9e12C ![]() 9e13C C: citing same article ( M: map data used to model this data |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Cytoplasmic dynein 1 ... , 3 types, 6 molecules ABCDEF
#1: Protein | Mass: 533083.250 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 71546.445 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein | Mass: 54173.156 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Dynein light chain ... , 3 types, 6 molecules GHIJKL
#4: Protein | Mass: 10934.576 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #5: Protein | Mass: 10381.899 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #6: Protein | Mass: 12461.996 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Protein , 1 types, 2 molecules OP
#7: Protein | Mass: 46709.984 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 3 types, 12 molecules 




#8: Chemical | ChemComp-ADP / #9: Chemical | #10: Chemical | ChemComp-MG / |
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-Details
Has ligand of interest | Y |
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Has protein modification | N |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Full-length human dynein-1 in phi-like comformation bound to a Lis1 dimer under Nde1-Lis1 condition Type: COMPLEX / Entity ID: #1-#7 / Source: RECOMBINANT |
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Molecular weight | Value: 1.5 MDa / Experimental value: YES |
Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.2 Details: 25 mM HEPES pH 7.2, 150 mM KCl, 1 mM MgCl2, 5 mM DTT, 3 mM ATP |
Specimen | Conc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 278 K |
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Electron microscopy imaging
Microscopy | Model: TFS GLACIOS |
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Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 45000 X / Calibrated magnification: 45000 X / Nominal defocus max: 2600 nm / Nominal defocus min: 1200 nm / Calibrated defocus min: 1200 nm / Calibrated defocus max: 2600 nm / Cs: 2.7 mm / C2 aperture diameter: 30 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||
3D reconstruction | Resolution: 5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 61684 / Symmetry type: POINT |