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Yorodumi- PDB-6f1t: Cryo-EM structure of two dynein tail domains bound to dynactin an... -
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-Basic information
Entry | Database: PDB / ID: 6f1t | |||||||||
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Title | Cryo-EM structure of two dynein tail domains bound to dynactin and BICDR1 | |||||||||
Components |
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Keywords | MOTOR PROTEIN / Cryo-EM / Complex / dynein/dynactin/BICDR / TDR | |||||||||
Function / homology | Function and homology information 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 / VEGFA-VEGFR2 Pathway / Cell-extracellular matrix interactions / RHO GTPases Activate WASPs and WAVEs / MAP2K and MAPK activation ...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 / 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 / vesicle transport along microtubule / 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 / dynactin 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 / stress granule assembly / cytoplasmic microtubule organization / Mitotic Prometaphase / cytoskeleton organization / regulation of mitotic spindle 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 Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) Homo sapiens (human) Sus scrofa (pig) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Urnavicius, L. / Lau, C.K. / Elshenawy, M.M. / Morales-Rios, E. / Motz, C. / Yildiz, A. / Carter, A.P. | |||||||||
Funding support | United Kingdom, 2items
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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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6f1t.cif.gz | 2.1 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6f1t.ent.gz | 1.7 MB | Display | PDB format |
PDBx/mmJSON format | 6f1t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f1/6f1t ftp://data.pdbj.org/pub/pdb/validation_reports/f1/6f1t | HTTPS FTP |
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-Related structure data
Related structure data | 4168MC 4169C 4170C 4171C 4172C 4177C 5owoC 6f1uC 6f1vC 6f1yC 6f1zC 6f38C 6f3aC 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 , 7 types, 17 molecules ABCDEFGIHJKLUklst
#1: Protein | Mass: 42670.688 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Details: ADP: Adenosine diphosphate ligand / Source: (natural) Sus scrofa (pig) / References: UniProt: F2Z5G5 #2: Protein | | Mass: 41782.660 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ATP: Adenosine triphosphate / Source: (natural) Sus scrofa (pig) / References: UniProt: Q6QAQ1 #3: Protein | | Mass: 43203.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ADP: Adenosine diphosphate / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LHK5 #4: Protein | | Mass: 33059.848 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0PFK5 #5: Protein | | Mass: 30669.768 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A9XFX6 #10: Protein | | Mass: 20703.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: D0G6S1 #22: Protein | Mass: 10934.576 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DYNLRB1, BITH, DNCL2A, DNLC2A, ROBLD1, HSPC162 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9NP97 |
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-Dynactin Subunit ... , 12 types, 14 molecules MNOPQRVYZabcdz
#6: Protein | Mass: 50144.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) | ||||||||||||||||||
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#7: Protein | Mass: 52612.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) | ||||||||||||||||||
#8: Protein | Mass: 5549.833 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) #9: Protein | Mass: 7422.140 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) #11: Protein | | Mass: 20150.533 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A286ZK88 #13: Protein | | Mass: 22400.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) #14: Protein | | Mass: 4443.468 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) #15: Protein | | Mass: 7377.013 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SKF9 #16: Protein | | Mass: 10000.866 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SKF9 #17: Protein/peptide | | Mass: 5581.965 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SKF9 #18: Protein/peptide | | Mass: 2880.144 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SKF9 #24: Protein | | Mass: 4528.573 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) |
-BICD family-like cargo adapter 1,BICD family-like cargo adapter 1,BICD family-like cargo adapter ... , 2 types, 2 molecules Xx
#12: Protein | Mass: 42423.039 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Bicdl1, Bicdr1, Ccdc64 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0JNT9 |
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#23: Protein | Mass: 42678.359 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Bicdl1, Bicdr1, Ccdc64 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0JNT9 |
-Cytoplasmic dynein 1 ... , 3 types, 12 molecules efmnghopijqr
#19: Protein | Mass: 119509.367 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DYNC1H1, DHC1, DNCH1, DNCL, DNECL, DYHC, KIAA0325 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q14204 #20: Protein | Mass: 68442.141 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DYNC1I2, DNCI2, DNCIC2 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q13409 #21: Protein | Mass: 54173.156 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DYNC1LI2, DNCLI2, LIC2 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O43237 |
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-Non-polymers , 2 types, 10 molecules
#25: Chemical | ChemComp-ADP / #26: 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
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Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.4 | ||||||||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy |
Image recording | Electron dose: 52 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: dev_2919: / Classification: refinement | ||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 205611 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Space: REAL / Target criteria: Cross-correlation coefficient 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 ...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. | ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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