+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5439 | |||||||||
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Title | Structural basis for microtubule binding and release by dynein | |||||||||
Map data | Construct of the high affinity dynein microtubule-binding domain fused to seryl-tRNA synthase-monomer | |||||||||
Sample |
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Keywords | dynein / microtubule bound / high affinity microtubule binding domain | |||||||||
Function / homology | Function and homology information COPI-independent Golgi-to-ER retrograde traffic / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / COPI-mediated anterograde transport / cilium movement / Aggrephagy / positive regulation of intracellular transport / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / regulation of metaphase plate congression ...COPI-independent Golgi-to-ER retrograde traffic / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / COPI-mediated anterograde transport / cilium movement / Aggrephagy / positive regulation of intracellular transport / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / regulation of metaphase plate congression / Resolution of Sister Chromatid Cohesion / establishment of spindle localization / positive regulation of spindle assembly / RHO GTPases Activate Formins / Separation of Sister Chromatids / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / Regulation of PLK1 Activity at G2/M Transition / manchette / P-body assembly / dynein complex / MHC class II antigen presentation / minus-end-directed microtubule motor activity / cytoplasmic dynein complex / retrograde axonal transport / dynein light intermediate chain binding / nuclear migration / positive regulation of axon guidance / dynein intermediate chain binding / cytoplasmic microtubule / microtubule-based process / cytoplasmic microtubule organization / stress granule assembly / regulation of mitotic spindle organization / axon cytoplasm / cellular response to interleukin-4 / Neutrophil degranulation / mitotic spindle organization / filopodium / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / microtubule cytoskeleton organization / microtubule cytoskeleton / double-stranded RNA binding / mitotic cell cycle / nuclear envelope / nervous system development / positive regulation of cold-induced thermogenesis / cell cortex / microtubule / protein heterodimerization activity / axon / cell division / GTPase activity / centrosome / neuronal cell body / ubiquitin protein ligase binding / GTP binding / ATP hydrolysis activity / ATP binding / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) / Bos taurus (cattle) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 9.7 Å | |||||||||
Authors | Redwine WB / Hernandez-Lopez R / Zou S / Huang J / Reck-Peterson SL / Leschziner AE | |||||||||
Citation | Journal: Science / Year: 2012 Title: Structural basis for microtubule binding and release by dynein. Authors: W B Redwine / R Hernandez-Lopez / S Zou / J Huang / S L Reck-Peterson / A E Leschziner / Abstract: Cytoplasmic dynein is a microtubule-based motor required for intracellular transport and cell division. Its movement involves coupling cycles of track binding and release with cycles of force- ...Cytoplasmic dynein is a microtubule-based motor required for intracellular transport and cell division. Its movement involves coupling cycles of track binding and release with cycles of force-generating nucleotide hydrolysis. How this is accomplished given the ~25 nanometers separating dynein's track- and nucleotide-binding sites is not understood. Here, we present a subnanometer-resolution structure of dynein's microtubule-binding domain bound to microtubules by cryo-electron microscopy that was used to generate a pseudo-atomic model of the complex with molecular dynamics. We identified large rearrangements triggered by track binding and specific interactions, confirmed by mutagenesis and single-molecule motility assays, which tune dynein's affinity for microtubules. Our results provide a molecular model for how dynein's binding to microtubules is communicated to the rest of the motor. | |||||||||
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_5439.map.gz | 336.1 KB | EMDB map data format | |
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Header (meta data) | emd-5439-v30.xml emd-5439.xml | 12.3 KB 12.3 KB | Display Display | EMDB header |
Images | emd_5439.png | 151.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5439 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5439 | HTTPS FTP |
-Related structure data
Related structure data | 3j1tMC 3j1uMC 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_5439.map.gz / Format: CCP4 / Size: 492.2 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Construct of the high affinity dynein microtubule-binding domain fused to seryl-tRNA synthase-monomer | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.988 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : high affinity construct of dynein microtubule-binding domain fuse...
Entire | Name: high affinity construct of dynein microtubule-binding domain fused to seryl-tRNA synthase monomer |
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Components |
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-Supramolecule #1000: high affinity construct of dynein microtubule-binding domain fuse...
Supramolecule | Name: high affinity construct of dynein microtubule-binding domain fused to seryl-tRNA synthase monomer type: sample / ID: 1000 / Number unique components: 2 |
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-Macromolecule #1: High affinity dynein microtubule binding domain
Macromolecule | Name: High affinity dynein microtubule binding domain / type: protein_or_peptide / ID: 1 / Recombinant expression: Yes |
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Source (natural) | Organism: Mus musculus (house mouse) / synonym: mouse |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Macromolecule #2: tubulin
Macromolecule | Name: tubulin / type: protein_or_peptide / ID: 2 / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: Bos taurus (cattle) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Concentration | 15 mg/mL |
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Buffer | pH: 8 / Details: 50 mM Tris-HCl, 1 mM MgCl2, 1 mM EGTA, 1 mM DTT |
Grid | Details: C-flat 2/2-2C holey carbon grids (Protochips) were glow-discharged for 20 seconds at 30 mA in an Edwards carbon evaporator. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 120 K / Instrument: FEI VITROBOT MARK IV Method: The solution was blotted manually, and the process of addition and blotting of SRS-MTBD was repeated a total of three times. The final blotting was done inside the humidity chamber of a ...Method: The solution was blotted manually, and the process of addition and blotting of SRS-MTBD was repeated a total of three times. The final blotting was done inside the humidity chamber of a Vitrobot Mark IV (FEI) at 22 Celsius. |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Electron beam | Acceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 63377 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.2 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 62000 |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN |
Temperature | Average: 100 K |
Date | Apr 10, 2011 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 6.35 µm / Number real images: 225 / Average electron dose: 15 e/Å2 / Bits/pixel: 8 |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: each particle |
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Final reconstruction | Applied symmetry - Helical parameters - Δz: 9.26 Å Applied symmetry - Helical parameters - Δ&Phi: 25.76 ° Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Frealign |
Details | Particles were aligned using customized scripts in SPIDER and 3D reconstruction was done using Frealign. |
-Atomic model buiding 1
Initial model | PDB ID: Chain - Chain ID: A |
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Software | Name: Chimera |
Details | Protocol: Rigid Body. The components of the complex were separately fitted by manual docking |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | PDB-3j1t: PDB-3j1u: |
-Atomic model buiding 2
Initial model | PDB ID: Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B |
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Software | Name: Chimera |
Details | Protocol: Rigid Body. The components of the complex were separately fitted by manual docking |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | PDB-3j1t: PDB-3j1u: |