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- PDB-9e12: Full-length human dynein-1 in phi comformation under Lis1 condition -
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Open data
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Basic information
Entry | Database: PDB / ID: 9000000000000 | ||||||
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Title | Full-length human dynein-1 in phi comformation under Lis1 condition | ||||||
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![]() | MOTOR PROTEIN / Dynein-1 / phi conformation | ||||||
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 / dynein intermediate chain binding / microtubule-based movement / nuclear migration / Macroautophagy / spermatid development / establishment of mitotic spindle orientation / tertiary granule membrane / ficolin-1-rich granule membrane / enzyme inhibitor activity / 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 / Mitotic Prometaphase / substantia nigra development / axon cytoplasm / 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 | ELECTRON MICROSCOPY / 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: Yang, J. / Zhang, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.9 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 269.7 KB | Display | |
Data in CIF | ![]() | 418.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 47381MC ![]() 9e0zC ![]() 9e10C ![]() 9e11C ![]() 9e13C ![]() 9e14C ![]() 47374 ![]() 48089 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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-Non-polymers , 3 types, 12 molecules 




#7: Chemical | ChemComp-ADP / #8: Chemical | #9: 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 comformation under Lis1 condition Type: COMPLEX / Entity ID: #1-#6 / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.2 |
Specimen | Conc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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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 | Name: PHENIX / Category: model refinement |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
3D reconstruction | Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 103097 / Symmetry type: POINT |