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- EMDB-2609: KIF14 Motor Domain Microtubule complex -

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Basic information

Entry
Database: EMDB / ID: 2609
TitleKIF14 Motor Domain Microtubule complex
Map datakinesin KIF14 mtor domain micerotubule complex
SampleKinesin KIF14 motor domain microtubule complex:
Kinesin KIF14 motor domain / Tubulin
KeywordsKinesin / Micotubule / Tubulin / KIF14 / Kinesin-3
SourceMus musculus (house mouse) / Bos taurus (cattle)
Methodhelical reconstruction / cryo EM / 15.5 Å resolution
AuthorsArora K / Talje L / Asenjo AB / Andersen P / Atchia K / Joshi M / Sosa H / Allingham JS / Kwok BH
CitationJournal: J. Mol. Biol. / Year: 2014
Title: KIF14 binds tightly to microtubules and adopts a rigor-like conformation.
Authors: Kritica Arora / Lama Talje / Ana B Asenjo / Parker Andersen / Kaleem Atchia / Monika Joshi / Hernando Sosa / John S Allingham / Benjamin H Kwok
Abstract: The mitotic kinesin motor protein KIF14 is essential for cytokinesis during cell division and has been implicated in cerebral development and a variety of human cancers. Here we show that the mouse ...The mitotic kinesin motor protein KIF14 is essential for cytokinesis during cell division and has been implicated in cerebral development and a variety of human cancers. Here we show that the mouse KIF14 motor domain binds tightly to microtubules and does not display typical nucleotide-dependent changes in this affinity. It also has robust ATPase activity but very slow motility. A crystal structure of the ADP-bound form of the KIF14 motor domain reveals a dramatically opened ATP-binding pocket, as if ready to exchange its bound ADP for Mg·ATP. In this state, the central β-sheet is twisted ~10° beyond the maximal amount observed in other kinesins. This configuration has only been seen in the nucleotide-free states of myosins-known as the "rigor-like" state. Fitting of this atomic model to electron density maps from cryo-electron microscopy indicates a distinct binding configuration of the motor domain to microtubules. We postulate that these properties of KIF14 are well suited for stabilizing midbody microtubules during cytokinesis.
DateDeposition: Mar 20, 2014 / Header (metadata) release: Apr 2, 2014 / Map release: Nov 19, 2014 / Last update: Nov 19, 2014

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_2609.map.gz (map file in CCP4 format, 941 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
68 pix
2 Å/pix.
= 136. Å
61 pix
2 Å/pix.
= 122. Å
58 pix
2 Å/pix.
= 116. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2 Å
Density
Contour Level:0.01 (by author), 0.01 (movie #1):
Minimum - Maximum-0.14100054 - 0.16273578
Average (Standard dev.)0.00518579 (0.04541813)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions615868
Origin14855148
Limit208112215
Spacing615868
CellA: 116 Å / B: 122 Å / C: 136 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z222
M x/y/z586168
origin x/y/z0.0000.0000.000
length x/y/z116.000122.000136.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS55148148
NC/NR/NS586168
D min/max/mean-0.1410.1630.005

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Supplemental data

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Sample components

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Entire Kinesin KIF14 motor domain microtubule complex

EntireName: Kinesin KIF14 motor domain microtubule complex / Number of components: 2

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Component #1: protein, Kinesin KIF14 motor domain

ProteinName: Kinesin KIF14 motor domain / Recombinant expression: Yes
SourceSpecies: Mus musculus (house mouse)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #2: protein, Tubulin

ProteinName: Tubulin / Recombinant expression: No
SourceSpecies: Bos taurus (cattle)

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Experimental details

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Sample preparation

SpecimenSpecimen state: helical array / Method: cryo EM
Helical parametersAxial symmetry: C1 (asymmetric) / Hand: RIGHT HANDED / Delta z: 5.40237 Å / Delta phi: 168.08788 deg.
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

ImagingMicroscope: FEI TECNAI 20 / Date: Nov 25, 2013
Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD / Defocus: 1000 - 2600 nm
Specimen HolderModel: GATAN LIQUID NITROGEN
CameraDetector: TVIPS TEMCAM-F415 (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 30

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Image processing

ProcessingMethod: helical reconstruction
Details: Initial reference map obtained by Fourier-Bessel reconstruction as implemented in SUPRIM & PHOELIX Single particle alignment, 3D reconstruction and refinement done using IHRSR, SPIDER and custom routines.
3D reconstructionSoftware: SUPRIM, PHOELIX, IHRSR, SPIDER, CTFFIND3, CUSTOM, (emglue.py)
CTF correction: Each Particle / Resolution: 15.5 Å / Resolution method: FSC 0.143, gold-standard

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Atomic model buiding

Modeling #1Software: Chimera / Refinement protocol: rigid body / Refinement space: REAL
Details: The 2 domains (tubulin heterodimer and KIF14 motor domain) were separately fitted. 1 nm resolution density maps of the atomic models were fitted within the cryo-em map using the global fit option of the fitmap command of the UCSF-CHIMERA program.
Input PDB model: 4OZQ
Modeling #2Refinement protocol: rigid body / Refinement space: REAL
Input PDB model: 1JFF

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