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- PDB-5gsy: Kinesin-8 motor, KIF19A, in the nucleotide-free state complexed w... -

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Basic information

Entry
Database: PDB / ID: 5gsy
TitleKinesin-8 motor, KIF19A, in the nucleotide-free state complexed with GDP-taxol microtubule
ComponentsKinesin-like protein KIF19
KeywordsMOTOR PROTEIN / Kinesin-8 / KIF19A / GDP-taxol-microtubule / Plus-end directed motor / Microtubule depolymerization
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
Kinesin-like protein / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Kinesin motor domain / Kinesin motor domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Kinesin-like protein KIF19
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 7 Å
AuthorsMorikawa, M. / Nitta, R. / Yajima, H. / Shigematsu, H. / Kikkawa, M. / Hirokawa, N.
Funding support Japan, 2items
OrganizationGrant numberCountry
MEXT23000013 Japan
MEXT15K08168 Japan
CitationJournal: 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
DepositionAug 17, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references
Revision 1.2Mar 27, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_image_scans
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Assembly

Deposited unit
K: Kinesin-like protein KIF19


Theoretical massNumber of molelcules
Total (without water)40,6361
Polymers40,6361
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16910 Å2

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Components

#1: Protein Kinesin-like protein KIF19


Mass: 40636.031 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 / Plasmid: pET21b
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
Strain (production host): BL21 / References: UniProt: Q99PT9

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: KIF19A motor domain complexed with GDP-taxol-MT / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
Plasmid: pET21b
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 300 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Cs: 2.7 mm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -25.71762 ° / Axial rise/subunit: 8.727751 Å / Axial symmetry: C1
3D reconstructionResolution: 7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 471380 / Details: High-resolution noise substitution was performed. / Symmetry type: HELICAL

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