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Yorodumi- EMDB-4177: Cryo-EM structure of two dynein tail domains bound to dynactin an... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4177 | |||||||||
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Title | Cryo-EM structure of two dynein tail domains bound to dynactin and HOOK3 | |||||||||
Map data | Cryo-EM map showing two dynein tails bound to dynactin and HOOK3 | |||||||||
Sample |
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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 / VEGFA-VEGFR2 Pathway / Cell-extracellular matrix interactions / RHO GTPases Activate WASPs and WAVEs / MAP2K and MAPK activation / dynactin complex ...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 / VEGFA-VEGFR2 Pathway / Cell-extracellular matrix interactions / RHO GTPases Activate WASPs and WAVEs / MAP2K and MAPK activation / dynactin complex / Clathrin-mediated endocytosis / transport along microtubule / visual behavior / dynein light chain binding / WASH complex / F-actin capping protein complex / dynein heavy chain binding / negative regulation of filopodium assembly / positive regulation of intracellular transport / regulation of metaphase plate congression / cellular response to cytochalasin B / establishment of spindle localization / ciliary tip / positive regulation of spindle assembly / regulation of transepithelial transport / structural constituent of postsynaptic actin cytoskeleton / morphogenesis of a polarized epithelium / Intraflagellar transport / postsynaptic actin cytoskeleton / protein localization to adherens junction / dense body / Tat protein binding / Neutrophil degranulation / P-body assembly / dynein complex / COPI-independent Golgi-to-ER retrograde traffic / apical protein localization / minus-end-directed microtubule motor activity / barbed-end actin filament capping / cytoplasmic dynein complex / retrograde axonal transport / adherens junction assembly / coronary vasculature development / dynein light intermediate chain binding / RHO GTPases activate IQGAPs / regulation of cell morphogenesis / RHO GTPases Activate Formins / regulation of lamellipodium assembly / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / COPI-independent Golgi-to-ER retrograde traffic / MHC class II antigen presentation / tight junction / nuclear migration / regulation of norepinephrine uptake / COPI-mediated anterograde transport / aorta development / NuA4 histone acetyltransferase complex / centrosome localization / regulation of synaptic vesicle endocytosis / ventricular septum development / microtubule motor activity / apical junction complex / establishment or maintenance of cell polarity / dynein intermediate chain binding / dynein complex binding / cortical cytoskeleton / positive regulation of double-strand break repair via homologous recombination / microtubule-based movement / nitric-oxide synthase binding / brush border / kinesin binding / calyx of Held / cytoplasmic microtubule / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / regulation of protein localization to plasma membrane / microtubule-based process / COPI-mediated anterograde transport / cytoplasmic microtubule organization / stress granule assembly / Mitotic Prometaphase / regulation of mitotic spindle organization / cytoskeleton organization / EML4 and NUDC in mitotic spindle formation / axon cytoplasm / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Resolution of Sister Chromatid Cohesion / Recruitment of NuMA to mitotic centrosomes / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Anchoring of the basal body to the plasma membrane / MHC class II antigen presentation / axonogenesis / sarcomere / AURKA Activation by TPX2 / cellular response to nerve growth factor stimulus / mitotic spindle organization / filopodium / cell motility / actin filament Similarity search - Function | |||||||||
Biological species | Sus scrofa (pig) / Homo sapiens (human) / Pig (pig) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.7 Å | |||||||||
Authors | Lau CK / Urnavicius L / Elshenawy MM / Morales-Rios E / Motz C / Yildiz A / Carter AP | |||||||||
Funding support | United Kingdom, 2 items
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Citation | Journal: Nature / Year: 2018 Title: Cryo-EM shows how dynactin recruits two dyneins for faster movement. Authors: Linas Urnavicius / Clinton K Lau / Mohamed M Elshenawy / Edgar Morales-Rios / Carina Motz / Ahmet Yildiz / Andrew P Carter / Abstract: Dynein and its cofactor dynactin form a highly processive microtubule motor in the presence of an activating adaptor, such as BICD2. Different adaptors link dynein and dynactin to distinct cargoes. ...Dynein and its cofactor dynactin form a highly processive microtubule motor in the presence of an activating adaptor, such as BICD2. Different adaptors link dynein and dynactin to distinct cargoes. Here we use electron microscopy and single-molecule studies to show that adaptors can recruit a second dynein to dynactin. Whereas BICD2 is biased towards recruiting a single dynein, the adaptors BICDR1 and HOOK3 predominantly recruit two dyneins. We find that the shift towards a double dynein complex increases both the force and speed of the microtubule motor. Our 3.5 Å resolution cryo-electron microscopy reconstruction of a dynein tail-dynactin-BICDR1 complex reveals how dynactin can act as a scaffold to coordinate two dyneins side-by-side. Our work provides a structural basis for understanding how diverse adaptors recruit different numbers of dyneins and regulate the motile properties of the dynein-dynactin transport machine. | |||||||||
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_4177.map.gz | 44.6 MB | EMDB map data format | |
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Header (meta data) | emd-4177-v30.xml emd-4177.xml | 51.7 KB 51.7 KB | Display Display | EMDB header |
Images | emd_4177.png | 79.6 KB | ||
Others | emd_4177_half_map_1.map.gz emd_4177_half_map_2.map.gz | 668.2 MB 669.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4177 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4177 | HTTPS FTP |
-Related structure data
Related structure data | 6f38MC 4168C 4169C 4170C 4171C 4172C 5owoC 6f1tC 6f1uC 6f1vC 6f1yC 6f1zC 6f3aC 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_4177.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM map showing two dynein tails bound to dynactin and HOOK3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.42 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: #1
File | emd_4177_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_4177_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Complex of two dynein tail domains bound to dynactin and HOOK3
+Supramolecule #1: Complex of two dynein tail domains bound to dynactin and HOOK3
+Supramolecule #2: Dynactin
+Supramolecule #3: Dynein
+Supramolecule #4: HOOK3
+Macromolecule #1: ARP1 actin related protein 1 homolog A
+Macromolecule #2: Actin, cytoplasmic 1
+Macromolecule #3: Actin related protein 10 homolog
+Macromolecule #4: Capping protein (Actin filament) muscle Z-line, alpha 1
+Macromolecule #5: F-actin capping protein beta subunit
+Macromolecule #6: Dynactin Subunit 2
+Macromolecule #7: Dynactin Subunit 2
+Macromolecule #8: Dynactin Subunit 3
+Macromolecule #9: Dynactin Subunit 2
+Macromolecule #10: Dynactin 6
+Macromolecule #11: Dynactin subunit 5
+Macromolecule #12: HOOK3
+Macromolecule #13: Dynactin Subunit 4
+Macromolecule #14: Dynactin Subunit 1
+Macromolecule #15: Dynactin subunit 2
+Macromolecule #16: Dynactin subunit 2
+Macromolecule #17: Dynactin subunit 2
+Macromolecule #18: Dynactin subunit 2
+Macromolecule #19: Cytoplasmic dynein 1 heavy chain 1
+Macromolecule #20: Cytoplasmic dynein 1 intermediate chain 2
+Macromolecule #21: Cytoplasmic dynein 1 light intermediate chain 2
+Macromolecule #22: Dynein light chain roadblock-type 1
+Macromolecule #23: Dynactin Subunit 1
+Macromolecule #24: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #25: ADENOSINE-5'-TRIPHOSPHATE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.2 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 45.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Software - Name: Gctf |
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Startup model | Type of model: EMDB MAP EMDB ID: Details: Model low pass filtered to 50 Angstroms |
Initial angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION |
Final angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 6.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 23407 |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Target criteria: Corellation Coefficient |
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Output model | PDB-6f38: |