+Open data
-Basic information
Entry | Database: PDB / ID: 5adx | |||||||||
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Title | CryoEM structure of dynactin complex at 4.0 angstrom resolution | |||||||||
Components |
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Keywords | STRUCTURAL PROTEIN / DYNEIN CO-FACTOR / ACTIN-LIKE FILAMENT / CELLULAR CARGO TRANSPORT | |||||||||
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 / Adherens junctions interactions / VEGFA-VEGFR2 Pathway / Cell-extracellular matrix interactions / RHO GTPases Activate WASPs and WAVEs / MAP2K and MAPK activation ...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 / Loss of proteins required for interphase microtubule organization from the centrosome / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / Recruitment of mitotic centrosome proteins and complexes / F-actin capping protein complex / negative regulation of filopodium assembly / actin cortical patch / structural constituent of postsynaptic actin cytoskeleton / dense body / dynein complex / Neutrophil degranulation / barbed-end actin filament capping / regulation of lamellipodium assembly / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / Recruitment of NuMA to mitotic centrosomes / COPI-mediated anterograde transport / NuA4 histone acetyltransferase complex / dynein complex binding / axon cytoplasm / 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 / actin filament binding / actin cytoskeleton / cell cortex / actin cytoskeleton organization / cytoskeleton / hydrolase activity / 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: 4 Å | |||||||||
Authors | Zhang, K. / Urnavicius, L. / Diamant, A.G. / Motz, C. / Schlage, M.A. / Yu, M. / Patel, N.A. / Robinson, C.V. / Carter, A.P. | |||||||||
Citation | Journal: Science / Year: 2015 Title: The structure of the dynactin complex and its interaction with dynein. Authors: Linas Urnavicius / Kai Zhang / Aristides G Diamant / Carina Motz / Max A Schlager / Minmin Yu / Nisha A Patel / Carol V Robinson / Andrew P Carter / Abstract: Dynactin is an essential cofactor for the microtubule motor cytoplasmic dynein-1. We report the structure of the 23-subunit dynactin complex by cryo-electron microscopy to 4.0 angstroms. Our ...Dynactin is an essential cofactor for the microtubule motor cytoplasmic dynein-1. We report the structure of the 23-subunit dynactin complex by cryo-electron microscopy to 4.0 angstroms. Our reconstruction reveals how dynactin is built around a filament containing eight copies of the actin-related protein Arp1 and one of β-actin. The filament is capped at each end by distinct protein complexes, and its length is defined by elongated peptides that emerge from the α-helical shoulder domain. A further 8.2 angstrom structure of the complex between dynein, dynactin, and the motility-inducing cargo adaptor Bicaudal-D2 shows how the translational symmetry of the dynein tail matches that of the dynactin filament. The Bicaudal-D2 coiled coil runs between dynein and dynactin to stabilize the mutually dependent interactions between all three components. | |||||||||
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 | 5adx.cif.gz | 1.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5adx.ent.gz | 926 KB | Display | PDB format |
PDBx/mmJSON format | 5adx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5adx_validation.pdf.gz | 806.4 KB | Display | wwPDB validaton report |
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Full document | 5adx_full_validation.pdf.gz | 816 KB | Display | |
Data in XML | 5adx_validation.xml.gz | 130.9 KB | Display | |
Data in CIF | 5adx_validation.cif.gz | 223.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ad/5adx ftp://data.pdbj.org/pub/pdb/validation_reports/ad/5adx | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-ACTIN RELATED PROTEIN ... , 2 types, 9 molecules ABCDEFGIJ
#1: Protein | Mass: 41959.930 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: BRAIN / References: UniProt: F2Z5G5 #3: Protein | | Mass: 46250.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: BRAIN / References: UniProt: I3LHK5 |
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-Protein , 4 types, 4 molecules HKLU
#2: Protein | Mass: 41193.043 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: BRAIN / References: UniProt: Q6QAQ1 |
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#4: Protein | Mass: 31777.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: BRAIN / References: UniProt: A0PFK5 |
#5: Protein | Mass: 30509.490 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: BRAIN / References: UniProt: D2JYW4 |
#10: Protein | Mass: 20703.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: BRAIN / References: UniProt: D0G6S1 |
-DYNACTIN SUBUNIT ... , 11 types, 14 molecules MNOPQRVYZzabcd
#6: Protein | Mass: 70144.070 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: BRAIN | ||||||||||||||||
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#7: Protein | Mass: 69633.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: BRAIN | ||||||||||||||||
#8: Protein | Mass: 7507.245 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: BRAIN #9: Protein | Mass: 7762.560 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: BRAIN #11: Protein | | Mass: 18164.301 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: BRAIN / References: UniProt: A0A0J9X291*PLUS #12: Protein | | Mass: 20698.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: BRAIN #13: Protein | Mass: 35676.918 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: BRAIN #14: Protein/peptide | | Mass: 5400.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: BRAIN / References: UniProt: A0A0J9X292*PLUS #15: Protein | | Mass: 7931.814 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: BRAIN / References: UniProt: A0A0J9X293*PLUS #16: Protein/peptide | | Mass: 3173.642 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: BRAIN / References: UniProt: A0A0J9X293*PLUS #17: Protein/peptide | | Mass: 2237.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: BRAIN / References: UniProt: A0A0J9X293*PLUS |
-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 / Source: NATURAL |
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Source (natural) | Organism: Sus scrofa (pig) / Tissue: Brain |
Buffer solution | Name: 50MM KCL, 25MM K2HPO4- KH2PO4, 1MM MGCL2,5MM DTT / pH: 6.5 / Details: 50MM KCL, 25MM K2HPO4- KH2PO4, 1MM MGCL2,5MM DTT |
Specimen | Conc.: 0.07 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: CARBON |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Details: LIQUID ENTHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS / Date: Sep 12, 2014 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 59000 X / Nominal defocus max: 5000 nm / Nominal defocus min: 2000 nm / Cs: 2.7 mm |
Specimen holder | Temperature: 90 K / Tilt angle max: 0 ° |
Image recording | Electron dose: 54 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
-Processing
EM software |
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Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||
3D reconstruction | Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 115044 / Refinement type: HALF-MAPS REFINED INDEPENDENTLY / Symmetry type: POINT | ||||||||||||
Refinement | Highest resolution: 4 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 4 Å
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