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Open data
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Basic information
Entry | Database: PDB / ID: 5afu | ||||||
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Title | Cryo-EM structure of dynein tail-dynactin-BICD2N complex | ||||||
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![]() | MOTOR PROTEIN / DYNEIN / DYNACTIN / BICD2 / MOTOR / TRANSPORT | ||||||
Function / homology | ![]() COPI-independent Golgi-to-ER retrograde traffic / 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 ...COPI-independent Golgi-to-ER retrograde traffic / 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 / F-actin capping protein complex / negative regulation of filopodium assembly / structural constituent of postsynaptic actin cytoskeleton / dense body / dynein complex / Neutrophil degranulation / coronary vasculature development / barbed-end actin filament capping / RHO GTPases activate IQGAPs / regulation of lamellipodium assembly / RHO GTPases Activate Formins / aorta development / Recruitment of NuMA to mitotic centrosomes / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / COPI-mediated anterograde transport / ventricular septum development / dynein complex binding / NuA4 histone acetyltransferase complex / 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 / nuclear membrane / cytoskeleton / hydrolase activity / axon / focal adhesion / centrosome / synapse / protein kinase binding / protein-containing complex / nucleoplasm / ATP binding / membrane / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.2 Å | ||||||
![]() | Urnavicius, L. / Zhang, K. / Diamant, A.G. / Motz, C. / Schlager, M.A. / Yu, M. / Patel, N.A. / Robinson, C.V. / Carter, A.P. | ||||||
![]() | ![]() 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
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.3 MB | Display | ![]() |
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PDB format | ![]() | 1 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 161.5 KB | Display | |
Data in CIF | ![]() | 273.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2860MC ![]() 2854C ![]() 2855C ![]() 2856C ![]() 2857C ![]() 2861C ![]() 2862C ![]() 5adxC ![]() 5afrC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Protein , 16 types, 27 molecules 123456ABCDEFGIHJKLMNOPQRUVb
#1: Protein | Mass: 30740.773 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||||||||||||||||||||||||||
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#2: Protein | Mass: 30570.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||||||||||||||||||||||||||
#3: Protein | Mass: 38900.738 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #4: Protein | Mass: 23421.752 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #5: Protein | Mass: 41959.930 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #6: Protein | | Mass: 41193.043 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #7: Protein | | Mass: 42141.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #8: Protein | | Mass: 31777.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #9: Protein | | Mass: 30509.490 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #10: Protein | | Mass: 49974.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #11: Protein | | Mass: 52442.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #12: Protein | Mass: 5549.833 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #13: Protein | Mass: 7422.140 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #14: Protein | | Mass: 18343.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #15: Protein | | Mass: 18178.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #19: Protein | | Mass: 7931.814 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-F-ACTIN-CAPPING PROTEIN SUBUNIT ... , 3 types, 3 molecules YZz
#16: Protein | Mass: 20698.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#17: Protein | Mass: 4443.468 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#22: Protein | Mass: 4528.573 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Protein/peptide , 3 types, 3 molecules acd
#18: Protein/peptide | Mass: 5400.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#20: Protein/peptide | Mass: 3019.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#21: Protein/peptide | Mass: 2237.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Non-polymers , 2 types, 10 molecules ![](data/chem/img/ADP.gif)
![](data/chem/img/ATP.gif)
![](data/chem/img/ATP.gif)
#23: Chemical | ChemComp-ADP / #24: Chemical | ChemComp-ATP / | |
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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 |
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Sample preparation
Component | Name: CRYO-EM STRUCTURE OF DYNEIN TAIL-DYNACTIN- BICD2N COMPLEX Type: COMPLEX Details: THE PARTICLES WERE SELECTED USING AN AUTOMATIC SELECTION PROGRAM. |
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Buffer solution | Name: 150MM KCL, 25MM HEPES-KOH, 1MM MGCL2, 0.1MM MGATP, 5MM DTT pH: 7.4 Details: 150MM KCL, 25MM HEPES-KOH, 1MM MGCL2, 0.1MM MGATP, 5MM DTT |
Specimen | Conc.: 0.08 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: HOLEY CARBON |
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Details: LIQUID ETHANE |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 47000 X / Calibrated magnification: 82353 X / Nominal defocus max: 8000 nm / Nominal defocus min: 3000 nm / Cs: 2.7 mm |
Specimen holder | Temperature: 100 K |
Image recording | Electron dose: 2 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
Image scans | Num. digital images: 14423 |
Radiation wavelength | Relative weight: 1 |
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Processing
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||
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3D reconstruction | Resolution: 8.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 85744 / Refinement type: HALF-MAPS REFINED INDEPENDENTLY / Symmetry type: POINT | ||||||||||||
Refinement | Highest resolution: 8.2 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 3.5 Å
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