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Yorodumi- PDB-5gsz: Crystal Structure of the KIF19A Motor Domain Complexed with Mg-ADP -
+Open data
-Basic information
Entry | Database: PDB / ID: 5gsz | |||||||||
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Title | Crystal Structure of the KIF19A Motor Domain Complexed with Mg-ADP | |||||||||
Components | Kinesin-like protein KIF19 | |||||||||
Keywords | MOTOR PROTEIN / kinesin / motor domain / Mg-ADP | |||||||||
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 | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.72 Å | |||||||||
Authors | Wang, D. / Nitta, R. / Hirokawa, N. | |||||||||
Funding support | Japan, 2items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5gsz.cif.gz | 112.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gsz.ent.gz | 92.1 KB | Display | PDB format |
PDBx/mmJSON format | 5gsz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gs/5gsz ftp://data.pdbj.org/pub/pdb/validation_reports/gs/5gsz | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 39669.016 Da / Num. of mol.: 1 / Fragment: UNP residues 1-353 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kif19, Kif19a / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: Q99PT9 |
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#2: Chemical | ChemComp-ADP / |
#3: Chemical | ChemComp-MG / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53.79 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: Ethylene Glycol, PEG8000, Tris-Bicine, Magnesium chloride, Calcium chloride |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Oct 12, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.71→50 Å / Num. obs: 12043 / % possible obs: 99.9 % / Redundancy: 13.6 % / Rmerge(I) obs: 0.132 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 2.71→2.81 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.995 / Rejects: 0 / % possible all: 99.3 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.72→34.32 Å / SU ML: 0.45 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 28.43 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 123.91 Å2 / Biso mean: 57.1 Å2 / Biso min: 30 Å2 | ||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.72→34.32 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4 / % reflection obs: 100 %
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