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Yorodumi- PDB-6f1u: N terminal region of dynein tail domains in complex with dynactin... -
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-Basic information
Entry | Database: PDB / ID: 6f1u | |||||||||
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Title | N terminal region of dynein tail domains in complex with dynactin filament and BICDR-1 | |||||||||
Components |
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Keywords | MOTOR PROTEIN / Cryo-EM / Complex / Cargo adaptor | |||||||||
Function / homology | Function and homology information Golgi to secretory granule transport / RHOD GTPase cycle / Factors involved in megakaryocyte development and platelet production / RHOF GTPase cycle / dynactin complex / Regulation of PLK1 Activity at G2/M Transition / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 ...Golgi to secretory granule transport / RHOD GTPase cycle / Factors involved in megakaryocyte development and platelet production / RHOF GTPase cycle / dynactin complex / Regulation of PLK1 Activity at G2/M Transition / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / Recruitment of mitotic centrosome proteins and complexes / transport along microtubule / F-actin capping protein complex / WASH complex / dynein light chain binding / positive regulation of intracellular transport / negative regulation of filopodium assembly / regulation of metaphase plate congression / dynein heavy chain binding / establishment of spindle localization / positive regulation of spindle assembly / actin cortical patch / vesicle transport along microtubule / dynein complex / minus-end-directed microtubule motor activity / COPI-independent Golgi-to-ER retrograde traffic / barbed-end actin filament capping / retrograde axonal transport / cytoplasmic dynein complex / dynein light intermediate chain binding / P-body assembly / regulation of cell morphogenesis / regulation of lamellipodium assembly / nuclear migration / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / Recruitment of NuMA to mitotic centrosomes / COPI-mediated anterograde transport / microtubule motor activity / dynein intermediate chain binding / microtubule-based movement / cytoplasmic microtubule / dynactin binding / microtubule-based process / COPI-mediated anterograde transport / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / cytoplasmic microtubule organization / stress granule assembly / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / regulation of mitotic spindle organization / Recruitment of mitotic centrosome proteins and complexes / cytoskeleton organization / axon cytoplasm / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / Resolution of Sister Chromatid Cohesion / sarcomere / AURKA Activation by TPX2 / mitotic spindle organization / filopodium / RHO GTPases Activate Formins / cell morphogenesis / small GTPase binding / Aggrephagy / HCMV Early Events / Separation of Sister Chromatids / azurophil granule lumen / Regulation of PLK1 Activity at G2/M Transition / neuron projection development / actin filament binding / positive regulation of cold-induced thermogenesis / actin binding / cell cortex / actin cytoskeleton organization / vesicle / microtubule / cell division / centrosome / Neutrophil degranulation / ATP hydrolysis activity / RNA binding / extracellular exosome / extracellular region / ATP binding / membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) Sus scrofa (pig) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 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 |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6f1u.cif.gz | 691.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6f1u.ent.gz | 548.3 KB | Display | PDB format |
PDBx/mmJSON format | 6f1u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6f1u_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6f1u_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6f1u_validation.xml.gz | 88.8 KB | Display | |
Data in CIF | 6f1u_validation.cif.gz | 140.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f1/6f1u ftp://data.pdbj.org/pub/pdb/validation_reports/f1/6f1u | HTTPS FTP |
-Related structure data
Related structure data | 4169MC 4168C 4170C 4171C 4172C 4177C 5owoC 6f1tC 6f1vC 6f1yC 6f1zC 6f38C 6f3aC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 4 types, 7 molecules BDFKLXx
#1: Protein | Mass: 42670.688 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: ADP: adenosine diphosphate / Source: (natural) Sus scrofa (pig) / References: UniProt: F2Z5G5 #2: Protein | | Mass: 33059.848 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0PFK5 #3: Protein | | Mass: 30566.627 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A9XFX6 #8: Protein | Mass: 65377.035 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Bicdl1, Bicdr1, Ccdc64 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0JNT9 |
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-Dynactin subunit ... , 2 types, 2 molecules cd
#4: 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 |
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#5: Protein/peptide | Mass: 2880.144 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SL58, UniProt: F1SKF9*PLUS |
-Cytoplasmic dynein 1 ... , 2 types, 4 molecules fmnh
#6: Protein | Mass: 136786.094 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DYNC1H1, DHC1, DNCH1, DNCL, DNECL, DYHC, KIAA0325 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q14204 #7: Protein | | Mass: 68442.141 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DYNC1I2, DNCI2, DNCIC2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q13409 |
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-Non-polymers , 1 types, 3 molecules
#9: Chemical |
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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 FIELD |
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: 3.4 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 | ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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