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Open data
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Basic information
Entry | Database: PDB / ID: 7z8g | ||||||||||||
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Title | Cytoplasmic dynein-1 motor domain | ||||||||||||
![]() | Cytoplasmic dynein 1 heavy chain 1 | ||||||||||||
![]() | STRUCTURAL PROTEIN / Dynein / dynactin / cargo transport / activating adaptor / cytoskeleton | ||||||||||||
Function / homology | ![]() positive regulation of intracellular transport / regulation of metaphase plate congression / establishment of spindle localization / axonemal dynein complex / positive regulation of spindle assembly / dynein complex / COPI-independent Golgi-to-ER retrograde traffic / P-body assembly / minus-end-directed microtubule motor activity / dynein light intermediate chain binding ...positive regulation of intracellular transport / regulation of metaphase plate congression / establishment of spindle localization / axonemal dynein complex / positive regulation of spindle assembly / dynein complex / COPI-independent Golgi-to-ER retrograde traffic / P-body assembly / minus-end-directed microtubule motor activity / dynein light intermediate chain binding / cytoplasmic dynein complex / retrograde axonal transport / nuclear migration / dynein intermediate chain binding / cytoplasmic microtubule / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / COPI-mediated anterograde transport / stress granule assembly / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / cytoplasmic microtubule organization / regulation of mitotic spindle organization / 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 / Anchoring of the basal body to the plasma membrane / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / AURKA Activation by TPX2 / mitotic spindle organization / filopodium / RHO GTPases Activate Formins / Aggrephagy / HCMV Early Events / Separation of Sister Chromatids / Regulation of PLK1 Activity at G2/M Transition / azurophil granule lumen / positive regulation of cold-induced thermogenesis / cell cortex / microtubule / cell division / centrosome / Neutrophil degranulation / ATP hydrolysis activity / RNA binding / extracellular exosome / extracellular region / ATP binding / membrane / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.52 Å | ||||||||||||
![]() | Chaaban, S. / Carter, A.P. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of dynein-dynactin on microtubules shows tandem adaptor binding. Authors: Sami Chaaban / Andrew P Carter / ![]() Abstract: Cytoplasmic dynein is a microtubule motor that is activated by its cofactor dynactin and a coiled-coil cargo adaptor. Up to two dynein dimers can be recruited per dynactin, and interactions between ...Cytoplasmic dynein is a microtubule motor that is activated by its cofactor dynactin and a coiled-coil cargo adaptor. Up to two dynein dimers can be recruited per dynactin, and interactions between them affect their combined motile behaviour. Different coiled-coil adaptors are linked to different cargos, and some share motifs known to contact sites on dynein and dynactin. There is limited structural information on how the resulting complex interacts with microtubules and how adaptors are recruited. Here we develop a cryo-electron microscopy processing pipeline to solve the high-resolution structure of dynein-dynactin and the adaptor BICDR1 bound to microtubules. This reveals the asymmetric interactions between neighbouring dynein motor domains and how they relate to motile behaviour. We found that two adaptors occupy the complex. Both adaptors make similar interactions with the dyneins but diverge in their contacts with each other and dynactin. Our structure has implications for the stability and stoichiometry of motor recruitment by cargos. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 572.7 KB | Display | ![]() |
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PDB format | ![]() | 449.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 100.8 KB | Display | |
Data in CIF | ![]() | 152.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 14550MC ![]() 7z8fC ![]() 7z8hC ![]() 7z8iC ![]() 7z8jC ![]() 7z8kC ![]() 7z8lC ![]() 7z8mC M: map data used to model this data C: citing same article ( |
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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
#1: Protein | Mass: 533055.125 Da / Num. of mol.: 1 / Mutation: R1567E, K1610E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-ADP / | ||
#3: Chemical | ChemComp-ATP / | ||
#4: Chemical | ChemComp-MG / | ||
#5: Chemical | Has ligand of interest | Y | |
-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: Dynein, cytoplasmic 1 / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1 / Source: RECOMBINANT | |||||||||||||||||||||||||||||||||||||||||||||
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Molecular weight | Value: 4 MDa / Experimental value: NO | |||||||||||||||||||||||||||||||||||||||||||||
Source (natural) | Organism: ![]() | |||||||||||||||||||||||||||||||||||||||||||||
Source (recombinant) | Organism: ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||
Buffer solution | pH: 7.2 | |||||||||||||||||||||||||||||||||||||||||||||
Buffer component |
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Specimen | 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: 293.15 K / Details: 20 second incubation |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 4000 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 3 sec. / Electron dose: 53 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 14 / Num. of real images: 88715 Details: Images were collected in movie-mode and fractionated into 53 movie frames |
EM imaging optics | Energyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV |
Image scans | Width: 5760 / Height: 4092 |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.52 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 351879 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL |