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Yorodumi- PDB-6f3a: Cryo-EM structure of a single dynein tail domain bound to dynacti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6f3a | |||||||||
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Title | Cryo-EM structure of a single dynein tail domain bound to dynactin and BICD2N | |||||||||
Components |
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Keywords | MOTOR PROTEIN / TDB / dynein/dynactin/BICD2 / complex | |||||||||
Function / homology | Function and homology information 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 ...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 / 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 / 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 / microtubule cytoskeleton organization / Aggrephagy / actin filament binding / Separation of Sister Chromatids / azurophil granule lumen Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) Sus scrofa (pig) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.2 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 | 6f3a.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6f3a.ent.gz | 951.4 KB | Display | PDB format |
PDBx/mmJSON format | 6f3a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6f3a_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 6f3a_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 6f3a_validation.xml.gz | 162.6 KB | Display | |
Data in CIF | 6f3a_validation.cif.gz | 291.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f3/6f3a ftp://data.pdbj.org/pub/pdb/validation_reports/f3/6f3a | HTTPS FTP |
-Related structure data
Related structure data | 2860M 4168C 4169C 4170C 4171C 4172C 4177C 5owoC 6f1tC 6f1uC 6f1vC 6f1yC 6f1zC 6f38C 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 , 8 types, 17 molecules ABCDEFGIHJKLUkl56
#1: Protein | Mass: 42670.688 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Details: ADP: Adenosine diphosphate / 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 #19: Protein | Mass: 10934.576 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DYNLRB1, BITH, DNCL2A, DNLC2A, ROBLD1, HSPC162 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9NP97 #21: Protein | Mass: 23421.752 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Spodoptera frugiperda (fall armyworm) |
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-Dynactin Subunit ... , 10 types, 14 molecules MNOPQRVYZabcdz
#6: Protein | Mass: 49974.707 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) | ||||||||||||||
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#7: Protein | Mass: 52442.777 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 #12: Protein | | Mass: 22485.607 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) #13: Protein | | Mass: 4443.468 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) #14: Protein | | Mass: 7578.217 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SKF9 #15: Protein | Mass: 10015.838 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1SKF9 #20: Protein | | Mass: 4528.573 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) |
-Cytoplasmic dynein 1 ... , 3 types, 5 molecules efghj
#16: Protein | Mass: 168318.781 Da / Num. of mol.: 2 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 #17: Protein | Mass: 68442.141 Da / Num. of mol.: 2 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 #18: Protein | | Mass: 54173.156 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DYNC1LI2, DNCLI2, LIC2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O43237 |
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-Non-polymers , 2 types, 10 molecules
#22: Chemical | ChemComp-ADP / #23: 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 | 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: 51 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: 8.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 85744 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Cross-correlation coefficient / Details: Took components from PDB 6F1T and fit into map | ||||||||||||||||||||||||
Refine LS restraints |
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