+Open data
-Basic information
Entry | Database: PDB / ID: 5afu | ||||||
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Title | Cryo-EM structure of dynein tail-dynactin-BICD2N complex | ||||||
Components |
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Keywords | MOTOR PROTEIN / DYNEIN / DYNACTIN / BICD2 / MOTOR / TRANSPORT | ||||||
Function / homology | Function and homology information 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 / actin cortical patch / structural constituent of postsynaptic actin cytoskeleton / dense body / dynein complex / Neutrophil degranulation / coronary vasculature development / barbed-end actin filament capping / regulation of lamellipodium assembly / RHO GTPases activate IQGAPs / 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 / mitotic spindle organization / axonogenesis / actin filament / cell motility / 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 / nuclear membrane / actin cytoskeleton organization / 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 | SUS SCROFA (pig) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.2 Å | ||||||
Authors | Urnavicius, L. / Zhang, K. / Diamant, A.G. / Motz, C. / Schlager, 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 | 5afu.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5afu.ent.gz | 1 MB | Display | PDB format |
PDBx/mmJSON format | 5afu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5afu_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 5afu_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 5afu_validation.xml.gz | 161.5 KB | Display | |
Data in CIF | 5afu_validation.cif.gz | 273.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/af/5afu ftp://data.pdbj.org/pub/pdb/validation_reports/af/5afu | 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 (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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) SUS SCROFA (pig) | ||||||||||||||||||||||||||
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#2: Protein | Mass: 30570.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) | ||||||||||||||||||||||||||
#3: Protein | Mass: 38900.738 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / References: UniProt: A0A0J9X2A1*PLUS #4: Protein | Mass: 23421.752 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) #5: 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 #6: 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 #7: Protein | | Mass: 42141.059 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: BRAIN / References: UniProt: I3LHK5 #8: 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 #9: 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: 49974.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: BRAIN #11: Protein | | Mass: 52442.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: BRAIN #12: Protein | Mass: 5549.833 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: BRAIN #13: Protein | Mass: 7422.140 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: BRAIN #14: Protein | | Mass: 18343.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: BRAIN / References: UniProt: D0G6S1*PLUS #15: Protein | | Mass: 18178.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: BRAIN / References: UniProt: A0A0J9X291*PLUS #19: 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 |
-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) SUS SCROFA (pig) / Organ: BRAIN |
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#17: Protein | Mass: 4443.468 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: BRAIN |
#22: Protein | Mass: 4528.573 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: BRAIN |
-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) SUS SCROFA (pig) / Organ: BRAIN / References: UniProt: A0A0J9X292*PLUS |
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#20: Protein/peptide | Mass: 3019.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: BRAIN / References: UniProt: A0A0J9X299*PLUS |
#21: 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: A0A0J9X295*PLUS |
-Non-polymers , 2 types, 10 molecules
#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 |
-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 |
-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: 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 |
-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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