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- EMDB-2766: Conserved mechanisms of microtubule-stimulated ADP release, ATP b... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-2766 | |||||||||
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Title | Conserved mechanisms of microtubule-stimulated ADP release, ATP binding, and force generation in transport kinesins | |||||||||
![]() | 13-protofilament microtubule-bound human kinesin-3 motor domain with AMPPNP | |||||||||
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Function / homology | ![]() neuronal dense core vesicle membrane / dense core granule cytoskeletal transport / anterograde neuronal dense core vesicle transport / retrograde neuronal dense core vesicle transport / regulation of dendritic spine development / cytoskeleton-dependent intracellular transport / regulation of dendritic spine morphogenesis / anterograde axonal transport / Kinesins / plus-end-directed microtubule motor activity ...neuronal dense core vesicle membrane / dense core granule cytoskeletal transport / anterograde neuronal dense core vesicle transport / retrograde neuronal dense core vesicle transport / regulation of dendritic spine development / cytoskeleton-dependent intracellular transport / regulation of dendritic spine morphogenesis / anterograde axonal transport / Kinesins / plus-end-directed microtubule motor activity / positive regulation of axon guidance / COPI-dependent Golgi-to-ER retrograde traffic / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Atherton J / Farabella I / Yu IM / Rosenfeld SS / Houdusse A / Topf M / Moores C | |||||||||
![]() | ![]() Title: Conserved mechanisms of microtubule-stimulated ADP release, ATP binding, and force generation in transport kinesins. Authors: Joseph Atherton / Irene Farabella / I-Mei Yu / Steven S Rosenfeld / Anne Houdusse / Maya Topf / Carolyn A Moores / ![]() ![]() ![]() Abstract: Kinesins are a superfamily of microtubule-based ATP-powered motors, important for multiple, essential cellular functions. How microtubule binding stimulates their ATPase and controls force generation ...Kinesins are a superfamily of microtubule-based ATP-powered motors, important for multiple, essential cellular functions. How microtubule binding stimulates their ATPase and controls force generation is not understood. To address this fundamental question, we visualized microtubule-bound kinesin-1 and kinesin-3 motor domains at multiple steps in their ATPase cycles--including their nucleotide-free states--at ∼ 7 Å resolution using cryo-electron microscopy. In both motors, microtubule binding promotes ordered conformations of conserved loops that stimulate ADP release, enhance microtubule affinity and prime the catalytic site for ATP binding. ATP binding causes only small shifts of these nucleotide-coordinating loops but induces large conformational changes elsewhere that allow force generation and neck linker docking towards the microtubule plus end. Family-specific differences across the kinesin-microtubule interface account for the distinctive properties of each motor. Our data thus provide evidence for a conserved ATP-driven mechanism for kinesins and reveal the critical mechanistic contribution of the microtubule interface. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 202.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 12.3 KB 12.3 KB | Display Display | ![]() |
Images | ![]() | 152.3 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4uxpMC ![]() 2765C ![]() 2767C ![]() 2768C ![]() 2769C ![]() 2770C ![]() 2771C ![]() 4uxoC ![]() 4uxrC ![]() 4uxsC ![]() 4uxtC ![]() 4uxyC ![]() 4uy0C M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | 13-protofilament microtubule-bound human kinesin-3 motor domain with AMPPNP | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : 13-protofilament microtubule-bound human kinesin-3 motor domain w...
Entire | Name: 13-protofilament microtubule-bound human kinesin-3 motor domain with AMPPNP |
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Components |
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-Supramolecule #1000: 13-protofilament microtubule-bound human kinesin-3 motor domain w...
Supramolecule | Name: 13-protofilament microtubule-bound human kinesin-3 motor domain with AMPPNP type: sample / ID: 1000 Oligomeric state: A kinesin motor domain binds to each alpha-beta tubulin heterodimer Number unique components: 3 |
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-Macromolecule #1: alpha tubulin
Macromolecule | Name: alpha tubulin / type: protein_or_peptide / ID: 1 / Oligomeric state: heterodimer / Recombinant expression: No |
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Source (natural) | Organism: ![]() ![]() ![]() |
Sequence | InterPro: Alpha tubulin |
-Macromolecule #2: beta tubulin
Macromolecule | Name: beta tubulin / type: protein_or_peptide / ID: 2 / Oligomeric state: heterodimer / Recombinant expression: No |
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Source (natural) | Organism: ![]() ![]() ![]() |
Sequence | InterPro: Beta tubulin, autoregulation binding site |
-Macromolecule #3: Kinesin-3 motor domain
Macromolecule | Name: Kinesin-3 motor domain / type: protein_or_peptide / ID: 3 / Name.synonym: Kif1A, Kin3 / Details: with bound AMPPNP / Oligomeric state: Monomer / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | InterPro: Kinesin motor domain, conserved site |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Buffer | pH: 6.8 Details: 20mM PIPES, 2mM MgCl2, 1mM EGTA, 2mM DTT, 2mM AMPPNP |
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Grid | Details: 400 mesh holey carbon grids, air glow discharged |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK I Method: Chamber at 24 degrees C, add microtubule droplet, blot 0.5 sec, add kinesin motor domain droplet, blot 3.5s. |
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Electron microscopy
Microscope | FEI POLARA 300 |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 100000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Sample stage | Specimen holder model: OTHER |
Temperature | Average: 90 K |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 150000 times magnification |
Date | Dec 10, 2012 |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Sampling interval: 15 µm / Number real images: 192 / Average electron dose: 20 e/Å2 |
Experimental equipment | ![]() Model: Tecnai Polara / Image courtesy: FEI Company |
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Image processing
CTF correction | Details: Frealign |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 7.0 Å / Resolution method: OTHER / Software - Name: Spider, Frealign Details: Pseudo-symmetry was utilised to generate the asymmetric unit at improved resolution Number images used: 97877 |
Details | The particles were selected interactively at the computer terminal |
-Atomic model buiding 1
Initial model | PDB ID: Chain - Chain ID: A |
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Software | Name: Chimera, Flex-EM |
Details | Initial model based on multiple PDBs rigid fitted in Chimera, then flexible fitting performed in Flex-EM (Topf et al., 2008) |
Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Target criteria: Cross-correlation |
Output model | ![]() PDB-4uxp: |
-Atomic model buiding 2
Initial model | PDB ID: Chain - Chain ID: K |
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Software | Name: Chimera, Flex-EM |
Details | Initial model based on multiple PDBs rigid fitted in Chimera, then flexible fitting performed in Flex-EM (Topf et al., 2008) |
Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Target criteria: Cross-correlation |
Output model | ![]() PDB-4uxp: |