+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2860 | |||||||||
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Title | Electron cryo-microscopy of dynein/dynactin/GFP-BICD2N complex | |||||||||
Map data | Reconstruction of dynein tail/dynactin/GFP-BICD2N complex. | |||||||||
Sample |
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Keywords | dynein / dynactin / BICD2 / motor / transport | |||||||||
Function / homology | Function and homology information COPI-independent Golgi-to-ER retrograde traffic / 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 ...COPI-independent Golgi-to-ER retrograde traffic / 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 / visual behavior / transport along microtubule / WASH complex / F-actin capping protein complex / positive regulation of intracellular transport / dynein light chain binding / negative regulation of filopodium assembly / regulation of metaphase plate congression / dynein heavy chain binding / establishment of spindle localization / positive regulation of spindle assembly / ciliary tip / actin cortical patch / structural constituent of postsynaptic actin cytoskeleton / Intraflagellar transport / dense body / dynein complex / Neutrophil degranulation / COPI-independent Golgi-to-ER retrograde traffic / coronary vasculature development / minus-end-directed microtubule motor activity / barbed-end actin filament capping / retrograde axonal transport / dynein light intermediate chain binding / cytoplasmic dynein complex / P-body assembly / regulation of cell morphogenesis / nuclear migration / 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 / centrosome localization / microtubule motor activity / dynein intermediate chain binding / dynein complex binding / microtubule-based movement / NuA4 histone acetyltransferase complex / cytoplasmic microtubule / microtubule-based process / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / COPI-mediated anterograde transport / cytoplasmic microtubule organization / stress fiber / stress granule assembly / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / regulation of mitotic spindle organization / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / axon cytoplasm / cytoskeleton organization / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / Resolution of Sister Chromatid Cohesion / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / sarcomere / AURKA Activation by TPX2 / mitotic spindle organization / axonogenesis / cellular response to nerve growth factor stimulus / filopodium / actin filament / cell motility / RHO GTPases Activate Formins / HCMV Early Events / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / cell morphogenesis / cilium / kinetochore Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Mus musculus (house mouse) / Sus scrofa domesticus (domestic pig) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.2 Å | |||||||||
Authors | Urnavicius L / Zhang K / Diamant AG / Motz C / Schlager MA / Yu M / Patel NA / Robinson CV / Carter AP | |||||||||
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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_2860.map.gz | 10.9 MB | EMDB map data format | |
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Header (meta data) | emd-2860-v30.xml emd-2860.xml | 10.8 KB 10.8 KB | Display Display | EMDB header |
Images | emd_2860.png | 2.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2860 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2860 | HTTPS FTP |
-Validation report
Summary document | emd_2860_validation.pdf.gz | 200.8 KB | Display | EMDB validaton report |
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Full document | emd_2860_full_validation.pdf.gz | 199.9 KB | Display | |
Data in XML | emd_2860_validation.xml.gz | 7.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2860 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2860 | HTTPS FTP |
-Related structure data
Related structure data | 5afuMC 6f3aM 6zo4M 2854C 2855C 2856C 2857C 2861C 2862C 5adxC 5afrC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_2860.map.gz / Format: CCP4 / Size: 300.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of dynein tail/dynactin/GFP-BICD2N complex. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.34 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Cryo-EM structure of dynein tail/dynactin/GFP-BICD2N
Entire | Name: Cryo-EM structure of dynein tail/dynactin/GFP-BICD2N |
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Components |
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-Supramolecule #1000: Cryo-EM structure of dynein tail/dynactin/GFP-BICD2N
Supramolecule | Name: Cryo-EM structure of dynein tail/dynactin/GFP-BICD2N / type: sample / ID: 1000 / Details: The sample was monodisperse / Number unique components: 3 |
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Molecular weight | Theoretical: 2.6 MDa |
-Macromolecule #1: Human cytoplasmic dynein 1 tail
Macromolecule | Name: Human cytoplasmic dynein 1 tail / type: protein_or_peptide / ID: 1 / Name.synonym: TDB / Number of copies: 1 / Recombinant expression: No |
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Source (natural) | Organism: Homo sapiens (human) / synonym: Human//Mouse / Location in cell: cytoplasm |
Molecular weight | Theoretical: 2.6 MDa |
-Macromolecule #2: mouse BICD2N
Macromolecule | Name: mouse BICD2N / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Recombinant expression: No |
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Source (natural) | Organism: Mus musculus (house mouse) / synonym: house mouse |
-Macromolecule #3: pig dynactin
Macromolecule | Name: pig dynactin / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Recombinant expression: No |
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Source (natural) | Organism: Sus scrofa domesticus (domestic pig) / synonym: domestic pig / Location in cell: cytoplasm |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.075 mg/mL |
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Buffer | pH: 7.4 Details: 150mM KCl, 25mM HEPES-KOH, 1mM MgCl2, 0.1mM MgATP, 5mM DTT |
Grid | Details: Quantifoil R1.2/1.3 400 mesh copper grid with thin carbon support, glow discharged |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 120 K / Instrument: FEI VITROBOT MARK III / Method: Blot for 3.5 seconds before plunging |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Average: 100 K |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 120,000 times magnification. |
Date | Jul 17, 2014 |
Image recording | Category: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Number real images: 4259 / Average electron dose: 1 e/Å2 / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 82353 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 8.0 µm / Nominal defocus min: 3.0 µm / Nominal magnification: 47000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Details | The particles were selected using an automatic selection program. |
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CTF correction | Details: Each particle |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 8.2 Å / Resolution method: OTHER / Software - Name: Relion / Number images used: 85744 |