+Open data
-Basic information
Entry | Database: PDB / ID: 6znl | |||||||||
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Title | Cryo-EM structure of the dynactin complex | |||||||||
Components |
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Keywords | STRUCTURAL PROTEIN / Dynactin / Complex / Scaffold / Cytoskeleton | |||||||||
Function / homology | Function and homology information RHOD GTPase cycle / Factors involved in megakaryocyte development and platelet production / 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 / Adherens junctions interactions / VEGFA-VEGFR2 Pathway / Cell-extracellular matrix interactions ...RHOD GTPase cycle / Factors involved in megakaryocyte development and platelet production / 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 / Adherens junctions interactions / VEGFA-VEGFR2 Pathway / Cell-extracellular matrix interactions / RHO GTPases Activate WASPs and WAVEs / MAP2K and MAPK activation / UCH proteinases / Clathrin-mediated endocytosis / RHOF GTPase cycle / 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 / WASH complex / F-actin capping protein complex / negative regulation of filopodium assembly / cytoskeleton-dependent cytokinesis / cell tip / structural constituent of postsynaptic actin cytoskeleton / microtubule plus-end / dense body / dynein complex / Neutrophil degranulation / barbed-end actin filament capping / microtubule plus-end binding / regulation of cell morphogenesis / RHO GTPases activate IQGAPs / regulation of lamellipodium assembly / RHO GTPases Activate Formins / nuclear migration / Recruitment of NuMA to mitotic centrosomes / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / microtubule associated complex / COPI-mediated anterograde transport / dynein complex binding / NuA4 histone acetyltransferase complex / establishment of mitotic spindle orientation / cleavage furrow / stress fiber / cytoplasmic microtubule organization / axon cytoplasm / cytoskeleton organization / centriole / sarcomere / axonogenesis / mitotic spindle organization / cell motility / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / cell morphogenesis / kinetochore / spindle pole / spindle / actin filament binding / actin cytoskeleton / nuclear envelope / actin binding / cell cortex / midbody / actin cytoskeleton organization / microtubule / cytoskeleton / hydrolase activity / cell division / axon / focal adhesion / centrosome / synapse / protein kinase binding / protein-containing complex / ATP binding / membrane / nucleus / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Sus scrofa (pig) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 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 | 6znl.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6znl.ent.gz | 974.9 KB | Display | PDB format |
PDBx/mmJSON format | 6znl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6znl_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 6znl_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 6znl_validation.xml.gz | 171.3 KB | Display | |
Data in CIF | 6znl_validation.cif.gz | 267.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zn/6znl ftp://data.pdbj.org/pub/pdb/validation_reports/zn/6znl | HTTPS FTP |
-Related structure data
Related structure data | 11313MC 6znmC 6znnC 6znoC 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 , 6 types, 13 molecules ABCDEFGIHJKLU
#1: Protein | Mass: 42670.688 Da / Num. of mol.: 8 / 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 #4: Protein | | Mass: 33059.848 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0PFK5 #5: Protein | | Mass: 30669.768 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A9XFX6 #8: Protein | | Mass: 20703.910 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, 10 molecules MNmnOoVYZz
#6: Protein | Mass: 44704.414 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A5G2QD80 #7: Protein | Mass: 21192.477 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SEC0 #9: Protein | | Mass: 20150.533 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A286ZK88 #10: Protein | | Mass: 52920.434 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1TB62 #11: Protein | Mass: 142547.156 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287B8J2*PLUS |
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-Non-polymers , 3 types, 13 molecules
#12: Chemical | ChemComp-ADP / #13: Chemical | ChemComp-ATP / | #14: 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 complex / Type: COMPLEX / Entity ID: #1-#11 / Source: NATURAL |
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Molecular weight | Value: 1 MDa / Experimental value: NO |
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 FIELD |
Image recording | Electron dose: 52 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
-Processing
EM software |
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Image processing | Details: All 4 image detectors used for reconstruction | |||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||
3D reconstruction | Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 336972 / Symmetry type: POINT | |||||||||
Atomic model building | Protocol: AB INITIO MODEL |