+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-7026 | |||||||||
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Title | KLP10A-AMPPNP in complex with curved tubulin and a microtubule | |||||||||
Map data | Map filtered with a B-factor of -100 A^2 | |||||||||
Sample |
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Keywords | kinesin 13 / microtubule / tubulin / depolymerization / MOTOR PROTEIN-STRUCTURAL PROTEIN complex | |||||||||
Function / homology | Function and homology information establishment of mitotic spindle asymmetry / establishment of meiotic spindle orientation / asymmetric protein localization involved in cell fate determination / plus-end specific microtubule depolymerization / cortical microtubule / meiotic spindle pole / mitotic spindle astral microtubule / centriole assembly / COPI-dependent Golgi-to-ER retrograde traffic / Kinesins ...establishment of mitotic spindle asymmetry / establishment of meiotic spindle orientation / asymmetric protein localization involved in cell fate determination / plus-end specific microtubule depolymerization / cortical microtubule / meiotic spindle pole / mitotic spindle astral microtubule / centriole assembly / COPI-dependent Golgi-to-ER retrograde traffic / Kinesins / mitotic chromosome movement towards spindle pole / kinetochore microtubule / meiotic spindle organization / spindle assembly involved in female meiosis I / non-motile cilium assembly / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Carboxyterminal post-translational modifications of tubulin / RHOH GTPase cycle / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / PKR-mediated signaling / The role of GTSE1 in G2/M progression after G2 checkpoint / Aggrephagy / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Separation of Sister Chromatids / plus-end-directed microtubule motor activity / meiotic spindle / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / Recruitment of NuMA to mitotic centrosomes / microtubule depolymerization / COPI-mediated anterograde transport / spindle organization / microtubule motor activity / kinesin complex / microtubule-based movement / mitotic spindle pole / centrosome duplication / cytoskeletal motor activity / microtubule-based process / chromosome, centromeric region / mitotic spindle organization / structural constituent of cytoskeleton / spindle / spindle pole / microtubule cytoskeleton organization / microtubule cytoskeleton / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / mitotic cell cycle / microtubule binding / microtubule / cell division / GTPase activity / centrosome / GTP binding / ATP hydrolysis activity / ATP binding / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Drosophila melanogaster (fruit fly) / Sus scrofa (pig) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.51 Å | |||||||||
Authors | Benoit MPMH / Asenjo AB | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Commun / Year: 2018 Title: Cryo-EM reveals the structural basis of microtubule depolymerization by kinesin-13s. Authors: Matthieu P M H Benoit / Ana B Asenjo / Hernando Sosa / Abstract: Kinesin-13s constitute a distinct group within the kinesin superfamily of motor proteins that promote microtubule depolymerization and lack motile activity. The molecular mechanism by which kinesin- ...Kinesin-13s constitute a distinct group within the kinesin superfamily of motor proteins that promote microtubule depolymerization and lack motile activity. The molecular mechanism by which kinesin-13s depolymerize microtubules and are adapted to perform a seemingly very different activity from other kinesins is still unclear. To address this issue, here we report the near atomic resolution cryo-electron microscopy (cryo-EM) structures of Drosophila melanogaster kinesin-13 KLP10A protein constructs bound to curved or straight tubulin in different nucleotide states. These structures show how nucleotide induced conformational changes near the catalytic site are coupled with movement of the kinesin-13-specific loop-2 to induce tubulin curvature leading to microtubule depolymerization. The data highlight a modular structure that allows similar kinesin core motor-domains to be used for different functions, such as motility or microtubule depolymerization. | |||||||||
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_7026.map.gz | 115.9 MB | EMDB map data format | |
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Header (meta data) | emd-7026-v30.xml emd-7026.xml | 22.5 KB 22.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_7026_fsc.xml | 21.5 KB | Display | FSC data file |
Images | emd_7026.png | 275.7 KB | ||
Masks | emd_7026_msk_1.map | 891.7 MB | Mask map | |
Filedesc metadata | emd-7026.cif.gz | 7.4 KB | ||
Others | emd_7026_half_map_1.map.gz emd_7026_half_map_2.map.gz | 294.5 MB 294.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-7026 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7026 | HTTPS FTP |
-Validation report
Summary document | emd_7026_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_7026_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_7026_validation.xml.gz | 29.3 KB | Display | |
Data in CIF | emd_7026_validation.cif.gz | 39.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7026 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7026 | HTTPS FTP |
-Related structure data
Related structure data | 6b0cMC 7027C 7028C 6b0iC 6b0lC C: citing same article (ref.) M: atomic model generated by this map |
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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_7026.map.gz / Format: CCP4 / Size: 891.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Map filtered with a B-factor of -100 A^2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.073 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_7026_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Half map (1) from the Gold Standard refinement
File | emd_7026_half_map_1.map | ||||||||||||
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Annotation | Half map (1) from the Gold Standard refinement | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map (2) from the Gold Standard refinement
File | emd_7026_half_map_2.map | ||||||||||||
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Annotation | Half map (2) from the Gold Standard refinement | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : KLP10A-AMPPNP motor in complex with curved tubulin and a microtubule
+Supramolecule #1: KLP10A-AMPPNP motor in complex with curved tubulin and a microtubule
+Supramolecule #2: KLP10A-AMPPNP motor
+Supramolecule #3: microtubule
+Macromolecule #1: Tubulin alpha-1B chain
+Macromolecule #2: Tubulin beta chain
+Macromolecule #3: Kinesin-like protein Klp10A
+Macromolecule #4: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #5: MAGNESIUM ION
+Macromolecule #6: GUANOSINE-5'-DIPHOSPHATE
+Macromolecule #7: TAXOL
+Macromolecule #8: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 6.8 Component:
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Grid | Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY | ||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-50 / Average electron dose: 1.25 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 46598 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 22500 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
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Output model | PDB-6b0c: |