+Open data
-Basic information
Entry | Database: PDB / ID: 7z8m | ||||||||||||
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Title | The pointed end complex of dynactin bound to BICDR1 | ||||||||||||
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 / retrograde axonal transport of mitochondrion / Gap junction degradation / Formation of annular gap junctions / Regulation of actin dynamics for phagocytic cup formation / EPHB-mediated forward signaling / VEGFA-VEGFR2 Pathway / Cell-extracellular matrix interactions / RHO GTPases Activate WASPs and WAVEs / MAP2K and MAPK activation ...Golgi to secretory granule transport / retrograde axonal transport of mitochondrion / Gap junction degradation / Formation of annular gap junctions / Regulation of actin dynamics for phagocytic cup formation / EPHB-mediated forward signaling / VEGFA-VEGFR2 Pathway / Cell-extracellular matrix interactions / RHO GTPases Activate WASPs and WAVEs / MAP2K and MAPK activation / COPI-independent Golgi-to-ER retrograde traffic / dynactin complex / Regulation of PLK1 Activity at G2/M Transition / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / Clathrin-mediated endocytosis / cellular response to cytochalasin B / regulation of transepithelial transport / structural constituent of postsynaptic actin cytoskeleton / morphogenesis of a polarized epithelium / vesicle transport along microtubule / postsynaptic actin cytoskeleton / protein localization to adherens junction / dense body / Tat protein binding / Neutrophil degranulation / dynein complex / apical protein localization / coronary vasculature development / adherens junction assembly / tight junction / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / Recruitment of NuMA to mitotic centrosomes / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / regulation of norepinephrine uptake / aorta development / COPI-mediated anterograde transport / regulation of synaptic vesicle endocytosis / ventricular septum development / NuA4 histone acetyltransferase complex / apical junction complex / establishment or maintenance of cell polarity / dynein complex binding / cortical cytoskeleton / nitric-oxide synthase binding / dynactin binding / kinesin binding / brush border / calyx of Held / positive regulation of double-strand break repair via homologous recombination / microtubule-based process / regulation of protein localization to plasma membrane / stress fiber / axon cytoplasm / sarcomere / axonogenesis / mitotic spindle organization / cell motility / actin filament / adherens junction / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Schaffer collateral - CA1 synapse / kinetochore / small GTPase binding / cytoplasmic ribonucleoprotein granule / neuron projection development / nucleosome / actin cytoskeleton / lamellipodium / cell cortex / nuclear membrane / cytoskeleton / hydrolase activity / regulation of cell cycle / ribonucleoprotein complex / axon / focal adhesion / centrosome / glutamatergic synapse / synapse / protein kinase binding / protein-containing complex / nucleoplasm / ATP binding / membrane / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Mus musculus (house mouse) Sus scrofa (pig) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.37 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 | 7z8m.cif.gz | 466.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7z8m.ent.gz | 362.3 KB | Display | PDB format |
PDBx/mmJSON format | 7z8m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z8/7z8m ftp://data.pdbj.org/pub/pdb/validation_reports/z8/7z8m | HTTPS FTP |
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-Related structure data
Related structure data | 14559MC 7z8fC 7z8gC 7z8hC 7z8iC 7z8jC 7z8kC 7z8lC 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
-Dynactin subunit ... , 3 types, 3 molecules MYV
#1: Protein | Mass: 44703.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1W6J2 |
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#4: Protein | Mass: 52920.434 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1TB62 |
#8: Protein | Mass: 20150.533 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A286ZK88 |
-Protein , 5 types, 6 molecules XUJGIH
#2: Protein | Mass: 65377.035 Da / Num. of mol.: 1 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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#3: Protein | Mass: 20703.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: D0G6S1 | ||
#5: Protein | Mass: 46250.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LHK5 | ||
#6: Protein | Mass: 42670.688 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F2Z5G5 #7: Protein | | Mass: 41782.660 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q6QAQ1 |
-Non-polymers , 4 types, 11 molecules
#9: Chemical | #10: Chemical | ChemComp-ATP / | #11: Chemical | ChemComp-MG / #12: Chemical | |
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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: 3.37 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 165019 / Symmetry type: POINT | |||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL |