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Yorodumi- EMDB-4168: Cryo-EM structure of two dynein tail domains bound to dynactin an... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4168 | |||||||||
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Title | Cryo-EM structure of two dynein tail domains bound to dynactin and BICDR1 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Cryo-EM / Complex / MOTOR PROTEIN / dynein/dynactin/BICDR / TDR | |||||||||
Function / homology | Function and homology information RHOD GTPase cycle / Factors involved in megakaryocyte development and platelet production / Golgi to secretory granule transport / 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 ...RHOD GTPase cycle / Factors involved in megakaryocyte development and platelet production / Golgi to secretory granule transport / 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 / vesicle transport along microtubule / structural constituent of postsynaptic actin cytoskeleton / Intraflagellar transport / dense body / dynein complex / Neutrophil degranulation / COPI-independent Golgi-to-ER retrograde traffic / 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 / 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 / centrosome localization / microtubule motor activity / dynein intermediate chain binding / dynein complex binding / microtubule-based movement / NuA4 histone acetyltransferase complex / cytoplasmic microtubule / dynactin binding / microtubule-based process / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / COPI-mediated anterograde transport / cytoplasmic microtubule organization / 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 / small GTPase binding / microtubule cytoskeleton organization Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) / Homo sapiens (human) / Sus scrofa (pig) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Urnavicius L / Lau CK | |||||||||
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_4168.map.gz | 31.9 MB | EMDB map data format | |
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Header (meta data) | emd-4168-v30.xml emd-4168.xml | 53.8 KB 53.8 KB | Display Display | EMDB header |
Images | emd_4168.png | 141.9 KB | ||
Filedesc metadata | emd-4168.cif.gz | 10.2 KB | ||
Others | emd_4168_additional_1.map.gz emd_4168_additional_2.map.gz | 290.3 MB 770.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4168 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4168 | HTTPS FTP |
-Validation report
Summary document | emd_4168_validation.pdf.gz | 204.8 KB | Display | EMDB validaton report |
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Full document | emd_4168_full_validation.pdf.gz | 203.9 KB | Display | |
Data in XML | emd_4168_validation.xml.gz | 8.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4168 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4168 | HTTPS FTP |
-Related structure data
Related structure data | 6f1tMC 4169C 4170C 4171C 4172C 4177C 5owoC 6f1uC 6f1vC 6f1yC 6f1zC 6f38C 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_4168.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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
-Additional map: #1
File | emd_4168_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: #2
File | emd_4168_additional_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Cryo-EM map of two dynein tail domains bound to dynactin and BICDR1
+Supramolecule #1: Cryo-EM map of two dynein tail domains bound to dynactin and BICDR1
+Supramolecule #2: BICD family-like cargo adapter 1
+Supramolecule #3: Dynein
+Supramolecule #4: Dynactin
+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: BICD family-like cargo adapter 1,BICD family-like cargo adapter 1...
+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,Cytoplasmic dynein 1 heavy cha...
+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: BICD family-like cargo adapter 1,BICD family-like cargo adapter 1...
+Macromolecule #24: Dynactin Subunit 1
+Macromolecule #25: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #26: 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: 7.4 |
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Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK III |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 52.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: EMDB MAP EMDB ID: Details: Initial model low pass filtered to 50 A |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 205611 |
Initial angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION |
Final angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION |
-Atomic model buiding 1
Details | Refinement of Dynein chains (chains f, h, j, m, o, s, t) performed using related maps. Coordinates from these chains were used for the other dynein chains, refining into 5 and 8 A maps, then removing sidechains. Dynactin and parts of dyneins refined into this 3.5 A map. |
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Refinement | Space: REAL / Target criteria: Cross-correlation coefficient |
Output model | PDB-6f1t: |