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Yorodumi- PDB-7z8i: The barbed end complex of dynactin bound to BICDR1 and the cytopl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7z8i | ||||||||||||
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Title | The barbed end complex of dynactin bound to BICDR1 and the cytoplasmic dynein tails (A2, B1, B2) | ||||||||||||
Components |
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Keywords | STRUCTURAL PROTEIN / Dynein / dynactin / cargo transport / activating adaptor / cytoskeleton | ||||||||||||
Function / homology | Function and homology information Golgi to secretory granule transport / transport along microtubule / dynein light chain binding / WASH complex / F-actin capping protein complex / dynein heavy chain binding / negative regulation of filopodium assembly / positive regulation of intracellular transport / regulation of metaphase plate congression / establishment of spindle localization ...Golgi to secretory granule transport / transport along microtubule / dynein light chain binding / WASH complex / F-actin capping protein complex / dynein heavy chain binding / negative regulation of filopodium assembly / positive regulation of intracellular transport / regulation of metaphase plate congression / establishment of spindle localization / positive regulation of spindle assembly / vesicle transport along microtubule / P-body assembly / dynein complex / COPI-independent Golgi-to-ER retrograde traffic / minus-end-directed microtubule motor activity / barbed-end actin filament capping / cytoplasmic dynein complex / retrograde axonal transport / dynein light intermediate chain binding / regulation of cell morphogenesis / regulation of lamellipodium assembly / nuclear migration / centrosome localization / microtubule motor activity / dynein intermediate chain binding / microtubule-based movement / dynactin binding / cytoplasmic microtubule / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / COPI-mediated anterograde transport / stress granule assembly / cytoplasmic microtubule organization / Mitotic Prometaphase / cytoskeleton organization / regulation of mitotic spindle organization / 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 / MHC class II antigen presentation / sarcomere / AURKA Activation by TPX2 / cellular response to nerve growth factor stimulus / mitotic spindle organization / filopodium / RHO GTPases Activate Formins / cell morphogenesis / microtubule cytoskeleton organization / kinetochore / small GTPase binding / Aggrephagy / HCMV Early Events / neuron projection development / Separation of Sister Chromatids / azurophil granule lumen / Regulation of PLK1 Activity at G2/M Transition / actin filament binding / late endosome / actin binding / positive regulation of cold-induced thermogenesis / cell cortex / actin cytoskeleton organization / vesicle / microtubule / cell division / centrosome / Neutrophil degranulation / ATP hydrolysis activity / RNA binding / extracellular exosome / extracellular region / ATP binding / membrane / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) Sus scrofa (pig) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||||||||
Authors | Chaaban, S. / Carter, A.P. | ||||||||||||
Funding support | United Kingdom, European Union, 3items
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Citation | Journal: Nature / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7z8i.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7z8i.ent.gz | 919.9 KB | Display | PDB format |
PDBx/mmJSON format | 7z8i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z8/7z8i ftp://data.pdbj.org/pub/pdb/validation_reports/z8/7z8i | HTTPS FTP |
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-Related structure data
Related structure data | 14552MC 7z8fC 7z8gC 7z8hC 7z8jC 7z8kC 7z8lC 7z8mC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 4 types, 10 molecules ABCDEFKLXx
#1: Protein | Mass: 42670.688 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F2Z5G5 #2: Protein | | Mass: 33059.848 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0PFK5 #3: Protein | | Mass: 30669.768 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A9XFX6 #4: Protein | Mass: 65377.035 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Bicdl1, Bicdr1, Ccdc64 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0JNT9 |
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-Cytoplasmic dynein 1 ... , 3 types, 7 molecules fmnhojr
#5: Protein | Mass: 533083.250 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DYNC1H1, DHC1, DNCH1, DNCL, DNECL, DYHC, KIAA0325 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q14204 #6: Protein | Mass: 71546.445 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DYNC1I2, DNCI2, DNCIC2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q13409 #7: Protein | Mass: 54173.156 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DYNC1LI2, DNCLI2, LIC2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O43237 |
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-Non-polymers , 2 types, 12 molecules
#8: Chemical | ChemComp-ADP / #9: Chemical | ChemComp-MG / |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
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Molecular weight |
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Source (natural) |
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Source (recombinant) |
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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 |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / 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 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 179660 / Symmetry type: POINT | |||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL |