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Open data
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Basic information
Entry | Database: PDB / ID: 6kio | |||||||||
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Title | Complex of yeast cytoplasmic dynein MTBD-High and MT without DTT | |||||||||
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![]() | MOTOR PROTEIN/STRUCTURAL PROTEIN / MOTOR PROTEIN-STRUCTURAL PROTEIN COMPLEX | |||||||||
Function / homology | ![]() karyogamy / establishment of mitotic spindle localization / astral microtubule / nuclear migration along microtubule / minus-end-directed microtubule motor activity / dynein light intermediate chain binding / cytoplasmic dynein complex / nuclear migration / spindle pole body / dynein intermediate chain binding ...karyogamy / establishment of mitotic spindle localization / astral microtubule / nuclear migration along microtubule / minus-end-directed microtubule motor activity / dynein light intermediate chain binding / cytoplasmic dynein complex / nuclear migration / spindle pole body / dynein intermediate chain binding / cytoplasmic microtubule / establishment of mitotic spindle orientation / mitotic sister chromatid segregation / cytoplasmic microtubule organization / Neutrophil degranulation / mitotic spindle organization / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / microtubule cytoskeleton organization / mitotic cell cycle / cell cortex / microtubule / hydrolase activity / GTPase activity / GTP binding / ATP hydrolysis activity / ATP binding / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.94 Å | |||||||||
![]() | Komori, Y. / Nishida, N. / Shimada, I. / Kikkawa, M. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for two-way communication between dynein and microtubules. Authors: Noritaka Nishida / Yuta Komori / Osamu Takarada / Atsushi Watanabe / Satoko Tamura / Satoshi Kubo / Ichio Shimada / Masahide Kikkawa / ![]() Abstract: The movements of cytoplasmic dynein on microtubule (MT) tracks is achieved by two-way communication between the microtubule-binding domain (MTBD) and the ATPase domain via a coiled-coil stalk, but ...The movements of cytoplasmic dynein on microtubule (MT) tracks is achieved by two-way communication between the microtubule-binding domain (MTBD) and the ATPase domain via a coiled-coil stalk, but the structural basis of this communication remains elusive. Here, we regulate MTBD either in high-affinity or low-affinity states by introducing a disulfide bond to the stalk and analyze the resulting structures by NMR and cryo-EM. In the MT-unbound state, the affinity changes of MTBD are achieved by sliding of the stalk α-helix by a half-turn, which suggests that structural changes propagate from the ATPase-domain to MTBD. In addition, MT binding induces further sliding of the stalk α-helix even without the disulfide bond, suggesting how the MT-induced conformational changes propagate toward the ATPase domain. Based on differences in the MT-binding surface between the high- and low-affinity states, we propose a potential mechanism for the directional bias of dynein movement on MT tracks. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 323.2 KB | Display | ![]() |
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PDB format | ![]() | 263.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 9996MC ![]() 9997C ![]() 6kiqC ![]() 6kjnC ![]() 6kjoC M: map data used to model this data C: citing same article ( |
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Similar structure data | |
EM raw data | ![]() Data size: 360.5 Data #1: Unaligned multi-frame micrographs of the complex of yeast cytoplasmic dynein MTBD-High and MT without DTT [micrographs - multiframe]) |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
#1: Protein | Mass: 47809.746 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: Protein | Mass: 15264.564 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Protein | Mass: 45959.980 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
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Sample preparation
Component | Name: MTBD-High/MT complex without DTT / Type: CELL / Entity ID: all / Source: MULTIPLE SOURCES | |||||||||||||||||||||||||
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Source (natural) | Organism: ![]() ![]() | |||||||||||||||||||||||||
Buffer solution | pH: 6.8 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Grid material: COPPER/RHODIUM / Grid type: Quantifoil R1.2/1.3 | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3250 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 1000 nm / Calibrated defocus max: 2500 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: OTHER |
Image recording | Average exposure time: 10 sec. / Electron dose: 54 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1820 |
Image scans | Width: 3838 / Height: 3710 / Movie frames/image: 40 / Used frames/image: 1-40 |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: -25.7561 ° / Axial rise/subunit: 9.20776 Å / Axial symmetry: C1 | |||||||||||||||||||||||||
Particle selection | Num. of particles selected: 76377 / Details: particles were collected using PyFilamentPicker | |||||||||||||||||||||||||
3D reconstruction | Resolution: 3.94 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 58999 / Details: FSCtrue was calculated to validate the resolution. / Symmetry type: HELICAL | |||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Correlation coefficient |