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Yorodumi- EMDB-26078: CaKip3[2-436]-L2-mutant(HsKHC) - AMP-PNP in complex with a microtubule -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26078 | ||||||||||||
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Title | CaKip3[2-436]-L2-mutant(HsKHC) - AMP-PNP in complex with a microtubule | ||||||||||||
Map data | Primary map, locally refined on the central asymmetric unit | ||||||||||||
Sample |
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Keywords | Kip3 / kinesin / motility / microtubule / tubulin / MOTOR PROTEIN | ||||||||||||
Function / homology | Function and homology information cytoplasm organization / cytolytic granule membrane / mitotic spindle astral microtubule / plus-end-directed vesicle transport along microtubule / mitocytosis / anterograde dendritic transport of neurotransmitter receptor complex / anterograde neuronal dense core vesicle transport / anterograde axonal protein transport / mitotic spindle midzone / retrograde neuronal dense core vesicle transport ...cytoplasm organization / cytolytic granule membrane / mitotic spindle astral microtubule / plus-end-directed vesicle transport along microtubule / mitocytosis / anterograde dendritic transport of neurotransmitter receptor complex / anterograde neuronal dense core vesicle transport / anterograde axonal protein transport / mitotic spindle midzone / retrograde neuronal dense core vesicle transport / vesicle transport along microtubule / lysosome localization / positive regulation of potassium ion transport / natural killer cell mediated cytotoxicity / 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 / Kinesins / RHO GTPases activate KTN1 / RHO GTPases activate IQGAPs / stress granule disassembly / RHO GTPases Activate Formins / Recruitment of NuMA to mitotic centrosomes / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / mitochondrion transport along microtubule / microtubule depolymerization / ciliary rootlet / COPI-mediated anterograde transport / COPI-dependent Golgi-to-ER retrograde traffic / centrosome localization / microtubule motor activity / kinesin complex / synaptic vesicle transport / Insulin processing / microtubule-based movement / mitotic sister chromatid segregation / centriolar satellite / axon cytoplasm / phagocytic vesicle / MHC class II antigen presentation / dendrite cytoplasm / regulation of membrane potential / axon guidance / positive regulation of synaptic transmission, GABAergic / positive regulation of protein localization to plasma membrane / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / cellular response to type II interferon / microtubule cytoskeleton organization / microtubule cytoskeleton / Signaling by ALK fusions and activated point mutants / mitotic cell cycle / microtubule binding / vesicle / microtubule / cadherin binding / GTPase activity / protein-containing complex binding / GTP binding / perinuclear region of cytoplasm / ATP hydrolysis activity / mitochondrion / ATP binding / identical protein binding / membrane / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | Candida albicans (yeast) / Sus scrofa (pig) | ||||||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.1 Å | ||||||||||||
Authors | Benoit MPMH / Asenjo AB / Hunter B / Allingham JS / Sosa H | ||||||||||||
Funding support | United States, Canada, 3 items
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Citation | Journal: Nat Commun / Year: 2022 Title: Kinesin-8-specific loop-2 controls the dual activities of the motor domain according to tubulin protofilament shape. Authors: Byron Hunter / Matthieu P M H Benoit / Ana B Asenjo / Caitlin Doubleday / Daria Trofimova / Corey Frazer / Irsa Shoukat / Hernando Sosa / John S Allingham / Abstract: Kinesin-8s are dual-activity motor proteins that can move processively on microtubules and depolymerize microtubule plus-ends, but their mechanism of combining these distinct activities remains ...Kinesin-8s are dual-activity motor proteins that can move processively on microtubules and depolymerize microtubule plus-ends, but their mechanism of combining these distinct activities remains unclear. We addressed this by obtaining cryo-EM structures (2.6-3.9 Å) of Candida albicans Kip3 in different catalytic states on the microtubule lattice and on a curved microtubule end mimic. We also determined a crystal structure of microtubule-unbound CaKip3-ADP (2.0 Å) and analyzed the biochemical activity of CaKip3 and kinesin-1 mutants. These data reveal that the microtubule depolymerization activity of kinesin-8 originates from conformational changes of its motor core that are amplified by dynamic contacts between its extended loop-2 and tubulin. On curved microtubule ends, loop-1 inserts into preceding motor domains, forming head-to-tail arrays of kinesin-8s that complement loop-2 contacts with curved tubulin and assist depolymerization. On straight tubulin protofilaments in the microtubule lattice, loop-2-tubulin contacts inhibit conformational changes in the motor core, but in the ADP-Pi state these contacts are relaxed, allowing neck-linker docking for motility. We propose that these tubulin shape-induced alternations between pro-microtubule-depolymerization and pro-motility kinesin states, regulated by loop-2, are the key to the dual activity of kinesin-8 motors. | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_26078.map.gz | 17 MB | EMDB map data format | |
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Header (meta data) | emd-26078-v30.xml emd-26078.xml | 24.2 KB 24.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_26078_fsc.xml | 11.3 KB | Display | FSC data file |
Images | emd_26078.png | 129.4 KB | ||
Masks | emd_26078_msk_1.map emd_26078_msk_2.map emd_26078_msk_3.map emd_26078_msk_4.map | 125 MB 125 MB 125 MB 125 MB | Mask map | |
Filedesc metadata | emd-26078.cif.gz | 8 KB | ||
Others | emd_26078_half_map_1.map.gz emd_26078_half_map_2.map.gz | 97.9 MB 97.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26078 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26078 | HTTPS FTP |
-Validation report
Summary document | emd_26078_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_26078_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_26078_validation.xml.gz | 18.3 KB | Display | |
Data in CIF | emd_26078_validation.cif.gz | 24.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26078 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26078 | HTTPS FTP |
-Related structure data
Related structure data | 7tr1MC 7lffC 7tqxC 7tqyC 7tqzC 7tr0C 7tr2C 7tr3C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_26078.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Primary map, locally refined on the central asymmetric unit | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.09 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_26078_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Mask #2
File | emd_26078_msk_2.map | ||||||||||||
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Density Histograms |
-Mask #3
File | emd_26078_msk_3.map | ||||||||||||
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Density Histograms |
-Mask #4
File | emd_26078_msk_4.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Half map from the gold Standard refinement
File | emd_26078_half_map_1.map | ||||||||||||
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Annotation | Half map from the gold Standard refinement | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map from the gold Standard refinement
File | emd_26078_half_map_2.map | ||||||||||||
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Annotation | Half map from the gold Standard refinement | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : CaKip3[2-436]-L2-mutant(HsKHC) - AMP-PNP in complex with a microtubule
+Supramolecule #1: CaKip3[2-436]-L2-mutant(HsKHC) - AMP-PNP in complex with a microtubule
+Supramolecule #2: CaKip3[2-436] with L2 swapped with the one of HsKHC, bound to AMP-PNP
+Supramolecule #3: 15R microtubule
+Macromolecule #1: Kinesin-like protein,Kinesin-1 heavy chain
+Macromolecule #2: Tubulin alpha-1B chain
+Macromolecule #3: Tubulin beta-2B chain
+Macromolecule #4: MAGNESIUM ION
+Macromolecule #5: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
+Macromolecule #6: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #7: GUANOSINE-5'-DIPHOSPHATE
+Macromolecule #8: TAXOL
-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 | Model: UltrAuFoil R2/2 / Material: GOLD / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING | ||||||||||||
Vitrification | Cryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV |
-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: 64.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.75 µm / Nominal defocus min: 0.8 µm |
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-7tr1: |