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Yorodumi- PDB-8fdt: Engineered human dynein motor domain in the microtubule-unbound s... -
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-Basic information
Entry | Database: PDB / ID: 8fdt | ||||||||||||
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Title | Engineered human dynein motor domain in the microtubule-unbound state with LIS1 complex in the buffer containing ATP-Vi | ||||||||||||
Components |
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Keywords | MOTOR PROTEIN / Dynein / motor domain / microtubule-unbound / LIS1 | ||||||||||||
Function / homology | Function and homology information corpus callosum morphogenesis / establishment of planar polarity of embryonic epithelium / microtubule cytoskeleton organization involved in establishment of planar polarity / ameboidal-type cell migration / interneuron migration / 1-alkyl-2-acetylglycerophosphocholine esterase complex / maintenance of centrosome location / microtubule sliding / selenocysteine biosynthetic process / microtubule organizing center organization ...corpus callosum morphogenesis / establishment of planar polarity of embryonic epithelium / microtubule cytoskeleton organization involved in establishment of planar polarity / ameboidal-type cell migration / interneuron migration / 1-alkyl-2-acetylglycerophosphocholine esterase complex / maintenance of centrosome location / microtubule sliding / selenocysteine biosynthetic process / microtubule organizing center organization / platelet activating factor metabolic process / acrosome assembly / radial glia-guided pyramidal neuron migration / cerebral cortex neuron differentiation / seryl-tRNA aminoacylation / serine-tRNA ligase / serine-tRNA ligase activity / positive regulation of intracellular transport / central region of growth cone / positive regulation of embryonic development / regulation of metaphase plate congression / establishment of centrosome localization / reelin-mediated signaling pathway / positive regulation of cytokine-mediated signaling pathway / cortical microtubule organization / establishment of spindle localization / astral microtubule / positive regulation of spindle assembly / nuclear membrane disassembly / layer formation in cerebral cortex / auditory receptor cell development / vesicle transport along microtubule / stem cell division / positive regulation of dendritic spine morphogenesis / stereocilium / myeloid leukocyte migration / dynein complex / COPI-independent Golgi-to-ER retrograde traffic / minus-end-directed microtubule motor activity / microtubule plus-end binding / negative regulation of JNK cascade / osteoclast development / retrograde axonal transport / dynein light intermediate chain binding / cytoplasmic dynein complex / P-body assembly / brain morphogenesis / motile cilium / nuclear migration / microtubule associated complex / kinesin complex / dynein intermediate chain binding / cochlea development / dynein complex binding / cytoplasmic microtubule / transmission of nerve impulse / cell leading edge / establishment of mitotic spindle orientation / germ cell development / dynactin binding / phospholipase binding / microtubule-based process / neuromuscular process controlling balance / protein secretion / neuroblast proliferation / positive regulation of axon extension / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / COPI-mediated anterograde transport / regulation of microtubule cytoskeleton organization / lipid catabolic process / cytoplasmic microtubule organization / stress granule assembly / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / JNK cascade / 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 / 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 / AURKA Activation by TPX2 / positive regulation of mitotic cell cycle / mitotic spindle organization / adult locomotory behavior / filopodium / hippocampus development / RHO GTPases Activate Formins / phosphoprotein binding / HCMV Early Events / neuron migration / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / kinetochore / cerebral cortex development / microtubule cytoskeleton organization Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) Thermus thermophilus (bacteria) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||||||||
Authors | Ton, W. / Wang, Y. / Chai, P. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Nat Struct Mol Biol / Year: 2023 Title: Microtubule-binding-induced allostery triggers LIS1 dissociation from dynein prior to cargo transport. Authors: William D Ton / Yue Wang / Pengxin Chai / Cisloynny Beauchamp-Perez / Nicholas T Flint / Lindsay G Lammers / Hao Xiong / Kai Zhang / Steven M Markus / Abstract: The lissencephaly-related protein LIS1 is a critical regulator of cytoplasmic dynein that governs motor function and intracellular localization (for example, to microtubule plus-ends). Although LIS1 ...The lissencephaly-related protein LIS1 is a critical regulator of cytoplasmic dynein that governs motor function and intracellular localization (for example, to microtubule plus-ends). Although LIS1 binding is required for dynein activity, its unbinding prior to initiation of cargo transport is equally important, since preventing dissociation leads to dynein dysfunction. To understand whether and how dynein-LIS1 binding is modulated, we engineered dynein mutants locked in a microtubule-bound (MT-B) or microtubule-unbound (MT-U) state. Whereas the MT-B mutant exhibits low LIS1 affinity, the MT-U mutant binds LIS1 with high affinity, and as a consequence remains almost irreversibly associated with microtubule plus-ends. We find that a monomeric motor domain is sufficient to exhibit these opposing LIS1 affinities, and that this is evolutionarily conserved between yeast and humans. Three cryo-EM structures of human dynein with and without LIS1 reveal microtubule-binding induced conformational changes responsible for this regulation. Our work reveals key biochemical and structural insight into LIS1-mediated dynein activation. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8fdt.cif.gz | 614 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8fdt.ent.gz | 491.2 KB | Display | PDB format |
PDBx/mmJSON format | 8fdt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8fdt_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
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Full document | 8fdt_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 8fdt_validation.xml.gz | 104.8 KB | Display | |
Data in CIF | 8fdt_validation.cif.gz | 155.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fd/8fdt ftp://data.pdbj.org/pub/pdb/validation_reports/fd/8fdt | HTTPS FTP |
-Related structure data
Related structure data | 29012MC 8fcyC 8fd6C 8fduC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 357459.125 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: residues 1458-3277 of dynein followed by residues 30-96 of serine-tRNA ligase, followed by residues 3412-4646 of dynein Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Thermus thermophilus (bacteria) Gene: DYNC1H1, DHC1, DNCH1, DNCL, DNECL, DYHC, KIAA0325, serS, TTHA0875 Strain: HB8 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q14204, UniProt: Q5SJX7, serine-tRNA ligase | ||||||||
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#2: Protein | Mass: 66423.547 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: SNAP tag present on C-terminus,SNAP tag present on C-terminus Source: (gene. exp.) Homo sapiens (human) / Gene: PAFAH1B1, LIS1, MDCR, MDS, PAFAHA / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P43034 #3: Chemical | ChemComp-ATP / | #4: Chemical | #5: Chemical | ChemComp-VO4 / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Engineered human dynein motor domain in microtubule-unbound state with LIS1 complex in the buffer containing ATP-Vi Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
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Molecular weight | Value: 0.49 MDa / Experimental value: YES |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) |
Buffer solution | pH: 7.4 Details: 50 mM Tris pH 7.4, 150 mM potassium acetate, 2 mM magnesium acetate, 1 mM EGTA, 1 mM DTT, and 0.1 mM Mg-ATP |
Specimen | Conc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277 K |
-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 / Nominal magnification: 105000 X / Calibrated magnification: 105000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1200 nm / Calibrated defocus min: 1200 nm / Calibrated defocus max: 3000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 40 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: UCSF ChimeraX / Version: 1.4/v9 / Classification: model building / URL: https://www.rbvi.ucsf.edu/chimerax/ / Os: macOS / Type: package | ||||||||||||||||||||||||||||||||||||
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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: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 53572 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL |