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Yorodumi- EMDB-9538: Kinesin-8 motor, KIF19A, in the nucleotide-free state complexed w... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9538 | |||||||||
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Title | Kinesin-8 motor, KIF19A, in the nucleotide-free state complexed with GDP-taxol microtubule | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Kinesin-8 / KIF19A / GDP-taxol-microtubule / Plus-end directed motor / Microtubule depolymerization / MOTOR PROTEIN | |||||||||
Function / homology | Function and homology information axonemal microtubule depolymerization / plus-end specific microtubule depolymerization / Kinesins / COPI-dependent Golgi-to-ER retrograde traffic / plus-end-directed microtubule motor activity / kinesin complex / microtubule-based movement / axoneme / cilium / microtubule binding ...axonemal microtubule depolymerization / plus-end specific microtubule depolymerization / Kinesins / COPI-dependent Golgi-to-ER retrograde traffic / plus-end-directed microtubule motor activity / kinesin complex / microtubule-based movement / axoneme / cilium / microtubule binding / microtubule / ATP hydrolysis activity / ATP binding Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 7.0 Å | |||||||||
Authors | Morikawa M / Nitta R / Yajima H / Shigematsu H / Kikkawa M / Hirokawa N | |||||||||
Funding support | Japan, 2 items
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Citation | Journal: Elife / Year: 2016 Title: Motility and microtubule depolymerization mechanisms of the Kinesin-8 motor, KIF19A. Authors: Doudou Wang / Ryo Nitta / Manatsu Morikawa / Hiroaki Yajima / Shigeyuki Inoue / Hideki Shigematsu / Masahide Kikkawa / Nobutaka Hirokawa / Abstract: The kinesin-8 motor, KIF19A, accumulates at cilia tips and controls cilium length. Defective KIF19A leads to hydrocephalus and female infertility because of abnormally elongated cilia. Uniquely among ...The kinesin-8 motor, KIF19A, accumulates at cilia tips and controls cilium length. Defective KIF19A leads to hydrocephalus and female infertility because of abnormally elongated cilia. Uniquely among kinesins, KIF19A possesses the dual functions of motility along ciliary microtubules and depolymerization of microtubules. To elucidate the molecular mechanisms of these functions we solved the crystal structure of its motor domain and determined its cryo-electron microscopy structure complexed with a microtubule. The features of KIF19A that enable its dual function are clustered on its microtubule-binding side. Unexpectedly, a destabilized switch II coordinates with a destabilized L8 to enable KIF19A to adjust to both straight and curved microtubule protofilaments. The basic clusters of L2 and L12 tether the microtubule. The long L2 with a characteristic acidic-hydrophobic-basic sequence effectively stabilizes the curved conformation of microtubule ends. Hence, KIF19A utilizes multiple strategies to accomplish the dual functions of motility and microtubule depolymerization by ATP hydrolysis. | |||||||||
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_9538.map.gz | 10.7 MB | EMDB map data format | |
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Header (meta data) | emd-9538-v30.xml emd-9538.xml | 10 KB 10 KB | Display Display | EMDB header |
Images | emd_9538.png | 188.5 KB | ||
Filedesc metadata | emd-9538.cif.gz | 5.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9538 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9538 | HTTPS FTP |
-Validation report
Summary document | emd_9538_validation.pdf.gz | 439.5 KB | Display | EMDB validaton report |
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Full document | emd_9538_full_validation.pdf.gz | 439.1 KB | Display | |
Data in XML | emd_9538_validation.xml.gz | 4.8 KB | Display | |
Data in CIF | emd_9538_validation.cif.gz | 5.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9538 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9538 | HTTPS FTP |
-Related structure data
Related structure data | 5gsyMC 5gszC 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_9538.map.gz / Format: CCP4 / Size: 12 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.284 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : KIF19A motor domain complexed with GDP-taxol-MT
Entire | Name: KIF19A motor domain complexed with GDP-taxol-MT |
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Components |
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-Supramolecule #1: KIF19A motor domain complexed with GDP-taxol-MT
Supramolecule | Name: KIF19A motor domain complexed with GDP-taxol-MT / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Mus musculus (house mouse) |
-Macromolecule #1: Kinesin-like protein KIF19
Macromolecule | Name: Kinesin-like protein KIF19 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 40.636031 KDa |
Recombinant expression | Organism: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others) |
Sequence | String: MKDSGDSKDQ QLMVALRVRP ISVAELEEGA TLIAHKMDEQ MVVLMDPMED PDDILRAHRS REKSYLFDVA FDFTATQEMV YQATTKSLI EGVISGYNAT VFAYGPTGCG KTYTMLGTDH EPGIYVRTLN DLFRAIEETS NDMEYEVSMS YLEIYNEMIR D LLNPALGY ...String: MKDSGDSKDQ QLMVALRVRP ISVAELEEGA TLIAHKMDEQ MVVLMDPMED PDDILRAHRS REKSYLFDVA FDFTATQEMV YQATTKSLI EGVISGYNAT VFAYGPTGCG KTYTMLGTDH EPGIYVRTLN DLFRAIEETS NDMEYEVSMS YLEIYNEMIR D LLNPALGY LELREDSKGV IQVAGITEVS TINAKEIMQL LMKGNRQRTQ EPTAANQTSS RSHAVLQVAV RQRSRVKNIL QE VRQGRLF MIDLAGSERA SQTQNRGQRM KEGAHINRSL LALGNCINAL SDKGSNKYIN YRDSKLTRLL KDSLGGNSRT VMI AHISPA STAFEESRNT LTYAGRAKNI RTRVKQNHHH HHHH UniProtKB: Kinesin-like protein KIF19 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 200 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 300 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TECNAI ARCTICA |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Helical parameters - Δz: 8.727751 Å Applied symmetry - Helical parameters - Δ&Phi: -25.717620 ° Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric) Resolution.type: BY AUTHOR / Resolution: 7.0 Å / Resolution method: FSC 0.143 CUT-OFF / Details: High-resolution noise substitution was performed. / Number images used: 471380 |
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Startup model | Type of model: PDB ENTRY |
Final angle assignment | Type: NOT APPLICABLE |