+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1604 | |||||||||
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Title | 9 Angstrom Structure of an AMPPNP Microtubule-Kinesin5 Complex | |||||||||
Map data | Microtubule-kinesin5 complex | |||||||||
Sample |
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Keywords | microtubule / tubulin / kinesin / kinesin-5 / KLP61F / Eg5 / mitosis | |||||||||
Function / homology | Function and homology information aster / plus-end directed microtubule sliding / fusome organization / fusome / COPI-dependent Golgi-to-ER retrograde traffic / Kinesins / centrosome separation / mitotic spindle microtubule / spindle elongation / microtubule bundle formation ...aster / plus-end directed microtubule sliding / fusome organization / fusome / COPI-dependent Golgi-to-ER retrograde traffic / Kinesins / centrosome separation / mitotic spindle microtubule / spindle elongation / microtubule bundle formation / positive regulation of Golgi to plasma membrane protein transport / plus-end-directed microtubule motor activity / mitotic centrosome separation / positive regulation of axon guidance / microtubule associated complex / kinesin complex / microtubule-based movement / mitotic spindle pole / Golgi organization / cytoskeletal motor activity / microtubule-based process / mitotic spindle assembly / protein secretion / mitotic spindle organization / spindle microtubule / mitotic spindle / structural constituent of cytoskeleton / spindle / microtubule cytoskeleton organization / microtubule cytoskeleton / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / mitotic cell cycle / nervous system development / microtubule binding / microtubule / hydrolase activity / protein heterodimerization activity / cell division / GTPase activity / GTP binding / Golgi apparatus / endoplasmic reticulum / ATP binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Bos taurus (cattle) / Drosophila melanogaster (fruit fly) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 9.4 Å | |||||||||
Authors | Bodey AJ / Kikkawa M / Moores CA | |||||||||
Citation | Journal: J Mol Biol / Year: 2009 Title: 9-Angström structure of a microtubule-bound mitotic motor. Authors: Andrew J Bodey / Masahide Kikkawa / Carolyn A Moores / Abstract: Kinesin-5 (K5) motors are important components of the microtubule (MT)-based cell division machinery and are targets for small-molecule inhibitors currently in cancer clinical trials. However, the ...Kinesin-5 (K5) motors are important components of the microtubule (MT)-based cell division machinery and are targets for small-molecule inhibitors currently in cancer clinical trials. However, the nature of the K5-MT interaction and the regulatory mechanisms that control it remain unclear. Using cryo-electron microscopy and image processing, we calculated the structure of a K5 motor bound to MTs at 9 A resolution, providing insight into this important interaction. Our reconstruction reveals the K5 motor domain in an ATP-like conformation in which MT binding induces the conserved nucleotide-sensing switch I and II loops to form a compact subdomain around the bound nucleotide. Our reconstruction also reveals a novel conformation for the K5-specific drug-binding loop 5, suggesting a possible role for it in switching K5s between force generation and diffusional modes of MT binding. Our data thus shed light on regulation of the interaction between spindle components important for chromosome segregation. | |||||||||
History |
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-Structure visualization
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
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Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_1604.map.gz | 11 MB | EMDB map data format | |
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Header (meta data) | emd-1604-v30.xml emd-1604.xml | 11.3 KB 11.3 KB | Display Display | EMDB header |
Images | 1604.gif | 131.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1604 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1604 | HTTPS FTP |
-Validation report
Summary document | emd_1604_validation.pdf.gz | 225.4 KB | Display | EMDB validaton report |
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Full document | emd_1604_full_validation.pdf.gz | 224.5 KB | Display | |
Data in XML | emd_1604_validation.xml.gz | 4.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1604 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1604 | HTTPS FTP |
-Related structure data
Related structure data | 2wbeMC 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_1604.map.gz / Format: CCP4 / Size: 12.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Microtubule-kinesin5 complex | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.4 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Microtubule-KLP61F complex with AMPPNP
Entire | Name: Microtubule-KLP61F complex with AMPPNP |
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Components |
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-Supramolecule #1000: Microtubule-KLP61F complex with AMPPNP
Supramolecule | Name: Microtubule-KLP61F complex with AMPPNP / type: sample / ID: 1000 / Number unique components: 2 |
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-Macromolecule #1: Microtubule
Macromolecule | Name: Microtubule / type: protein_or_peptide / ID: 1 / Name.synonym: Microtubule / Recombinant expression: No / Database: NCBI |
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Source (natural) | Organism: Bos taurus (cattle) / synonym: cattle / Tissue: Brain |
-Macromolecule #2: KLP61F
Macromolecule | Name: KLP61F / type: protein_or_peptide / ID: 2 / Name.synonym: KLP61F / Recombinant expression: Yes |
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Source (natural) | Organism: Drosophila melanogaster (fruit fly) / synonym: Fruit fly |
Molecular weight | Theoretical: 42 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant plasmid: pET-15b-TEV |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 6.8 Details: 80mM PIPES, 150mM NaCl, 7mM MgCl2, 1mM EGTA, 1mM beta-mercaptoethanol |
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Grid | Details: Quantifoil grid |
Vitrification | Cryogen name: ETHANE / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: Home made / Method: Blot for 2-3 seconds before plunging |
-Electron microscopy
Microscope | FEI TECNAI F20 |
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Alignment procedure | Legacy - Astigmatism: Astigmatism corrected at 150,000 times magnification |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7.0 µm / Number real images: 24 / Average electron dose: 10 e/Å2 / Bits/pixel: 12 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 50000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.94 µm / Nominal defocus min: 1.08 µm / Nominal magnification: 50000 |
Sample stage | Specimen holder: Single tilt cryo / Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.4 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Ruby-Helix |
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CTF correction | Details: Phase flipping, Wiener |
-Atomic model buiding 1
Initial model | PDB ID: |
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Software | Name: UCSF Chimera |
Details | Protocol: Rigid body. KLP61F, alpha-tubulin and beta-tubulin were all fitted separately |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | PDB-2wbe: |
-Atomic model buiding 2
Initial model | PDB ID: |
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Software | Name: UCSF Chimera |
Details | Protocol: Rigid body. KLP61F, alpha-tubulin and beta-tubulin were all fitted separately |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | PDB-2wbe: |