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- EMDB-9538: Kinesin-8 motor, KIF19A, in the nucleotide-free state complexed w... -

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Basic information

Entry
Database: EMDB / ID: EMD-9538
TitleKinesin-8 motor, KIF19A, in the nucleotide-free state complexed with GDP-taxol microtubule
Map data
Sample
  • Organelle or cellular component: KIF19A motor domain complexed with GDP-taxol-MT
    • Protein or peptide: Kinesin-like protein KIF19
KeywordsKinesin-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 / MHC class II antigen presentation / plus-end-directed microtubule motor activity / microtubule-based movement / axoneme / microtubule binding / microtubule ...axonemal microtubule depolymerization / plus-end specific microtubule depolymerization / Kinesins / COPI-dependent Golgi-to-ER retrograde traffic / MHC class II antigen presentation / plus-end-directed microtubule motor activity / microtubule-based movement / axoneme / microtubule binding / microtubule / cilium / ATP binding
Similarity search - Function
Kinesin-like protein / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / 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)
Methodhelical reconstruction / cryo EM / Resolution: 7.0 Å
AuthorsMorikawa M / Nitta R / Yajima H / Shigematsu H / Kikkawa M / Hirokawa N
Funding support Japan, 2 items
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 25, 2016-
Header (metadata) releaseSep 21, 2016-
Map releaseSep 28, 2016-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.3
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  • Surface view colored by cylindrical radius
  • Surface level: 3.3
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  • Surface view with fitted model
  • Atomic models: PDB-5gsy
  • Surface level: 3.3
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5gsy
  • Surface level: 3.3
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5gsy
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9538.png

Downloads & links

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Map

FileDownload / File: emd_9538.map.gz / Format: CCP4 / Size: 12 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.28 Å/pix.
x 192 pix.
= 246.528 Å		1.28 Å/pix.
x 128 pix.
= 164.352 Å		1.28 Å/pix.
x 128 pix.
= 164.352 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.284 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.3 / Movie #1: 3.3
Minimum - Maximum-3.3513227 - 10.942875000000001
Average (Standard dev.)1.2481178 (±2.7958586)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin256256192
Dimensions128128192
Spacing128128192
CellA: 164.352 Å / B: 164.352 Å / C: 246.52802 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.2841.2841.284
M x/y/z128128192
origin x/y/z0.0000.0000.000
length x/y/z164.352164.352246.528
α/β/γ90.00090.00090.000
start NX/NY/NZ-152-37
NX/NY/NZ998271
MAP C/R/S123
start NC/NR/NS256256192
NC/NR/NS128128192
D min/max/mean-3.35110.9431.248

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Supplemental data

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Sample components

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Entire : KIF19A motor domain complexed with GDP-taxol-MT

EntireName: KIF19A motor domain complexed with GDP-taxol-MT
Components
  • Organelle or cellular component: KIF19A motor domain complexed with GDP-taxol-MT
    • Protein or peptide: Kinesin-like protein KIF19

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Supramolecule #1: KIF19A motor domain complexed with GDP-taxol-MT

SupramoleculeName: KIF19A motor domain complexed with GDP-taxol-MT / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Kinesin-like protein KIF19

MacromoleculeName: Kinesin-like protein KIF19 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 40.636031 KDa
Recombinant expressionOrganism: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
SequenceString: 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

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 300 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied 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
Startup modelType of model: PDB ENTRY
Final angle assignmentType: NOT APPLICABLE

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