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Yorodumi- PDB-6zno: The pointed end complex of dynactin with the p150 projection docked -
+Open data
-Basic information
Entry | Database: PDB / ID: 6zno | |||||||||
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Title | The pointed end complex of dynactin with the p150 projection docked | |||||||||
Components |
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Keywords | STRUCTURAL PROTEIN / Dynactin / Complex / Scaffold / Cytoskeleton | |||||||||
Function / homology | Function and homology information 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 / dynactin complex ...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 / dynactin complex / Clathrin-mediated endocytosis / cellular response to cytochalasin B / regulation of transepithelial transport / structural constituent of postsynaptic actin cytoskeleton / morphogenesis of a polarized epithelium / postsynaptic actin cytoskeleton / protein localization to adherens junction / dense body / Tat protein binding / Neutrophil degranulation / dynein complex / apical protein localization / adherens junction assembly / coronary vasculature development / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / COPI-independent Golgi-to-ER retrograde traffic / MHC class II antigen presentation / tight junction / regulation of norepinephrine uptake / COPI-mediated anterograde transport / aorta development / NuA4 histone acetyltransferase complex / regulation of synaptic vesicle endocytosis / ventricular septum development / apical junction complex / establishment or maintenance of cell polarity / dynein complex binding / cortical cytoskeleton / positive regulation of double-strand break repair via homologous recombination / nitric-oxide synthase binding / brush border / kinesin binding / calyx of Held / regulation of protein localization to plasma membrane / microtubule-based process / stress fiber / axon cytoplasm / axonogenesis / sarcomere / mitotic spindle organization / actin filament / cell motility / adherens junction / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Schaffer collateral - CA1 synapse / cytoplasmic ribonucleoprotein granule / kinetochore / nucleosome / actin cytoskeleton / lamellipodium / cell cortex / nuclear membrane / microtubule / cytoskeleton / regulation of cell cycle / hydrolase activity / 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 | Sus scrofa (pig) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.8 Å | |||||||||
Authors | Lau, C.K. / Lacey, S.E. / Carter, A.P. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: EMBO J / Year: 2021 Title: Cryo-EM reveals the complex architecture of dynactin's shoulder region and pointed end. Authors: Clinton K Lau / Francis J O'Reilly / Balaji Santhanam / Samuel E Lacey / Juri Rappsilber / Andrew P Carter / Abstract: Dynactin is a 1.1 MDa complex that activates the molecular motor dynein for ultra-processive transport along microtubules. In order to do this, it forms a tripartite complex with dynein and a coiled- ...Dynactin is a 1.1 MDa complex that activates the molecular motor dynein for ultra-processive transport along microtubules. In order to do this, it forms a tripartite complex with dynein and a coiled-coil adaptor. Dynactin consists of an actin-related filament whose length is defined by its flexible shoulder domain. Despite previous cryo-EM structures, the molecular architecture of the shoulder and pointed end of the filament is still poorly understood due to the lack of high-resolution information in these regions. Here we combine multiple cryo-EM datasets and define precise masking strategies for particle signal subtraction and 3D classification. This overcomes domain flexibility and results in high-resolution maps into which we can build the shoulder and pointed end. The unique architecture of the shoulder securely houses the p150 subunit and positions the four identical p50 subunits in different conformations to bind dynactin's filament. The pointed end map allows us to build the first structure of p62 and reveals the molecular basis for cargo adaptor binding to different sites at the pointed end. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6zno.cif.gz | 458.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zno.ent.gz | 369.2 KB | Display | PDB format |
PDBx/mmJSON format | 6zno.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zn/6zno ftp://data.pdbj.org/pub/pdb/validation_reports/zn/6zno | HTTPS FTP |
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-Related structure data
Related structure data | 11319MC 6znlC 6znmC 6znnC 6zo4C C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 4 types, 5 molecules GIHJU
#1: Protein | Mass: 42670.688 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F2Z5G5 #2: Protein | | Mass: 41782.660 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q6QAQ1 #3: Protein | | Mass: 46250.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LHK5 #5: Protein | | Mass: 18103.799 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: D0G6S1 |
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-Dynactin subunit ... , 5 types, 5 molecules MVYZz
#4: Protein | Mass: 44704.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A5G2QD80 |
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#6: Protein | Mass: 20150.533 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A286ZK88 |
#7: 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: 16102.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) |
#9: Protein | Mass: 16017.708 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) |
-Non-polymers , 3 types, 7 molecules
#10: Chemical | #11: Chemical | ChemComp-ATP / | #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 | Name: Dynactin / Type: COMPLEX Details: Signal for the shoulder and barbed end has been subtracted Entity ID: #1-#9 / Source: NATURAL |
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Source (natural) | Organism: Sus scrofa (pig) |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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 | ||||||||||||
Image recording |
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-Processing
Image processing | Details: Data from both detectors were combined |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
3D reconstruction | Resolution: 6.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 20037 / Symmetry type: POINT |