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- EMDB-2609: KIF14 Motor Domain Microtubule complex -

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Basic information

Entry
Database: EMDB / ID: EMD-2609
TitleKIF14 Motor Domain Microtubule complex
Map datakinesin KIF14 mtor domain micerotubule complex
Sample
  • Sample: Kinesin KIF14 motor domain microtubule complex
  • Protein or peptide: Kinesin KIF14 motor domain
  • Protein or peptide: Tubulin
KeywordsKinesin / Micotubule / Tubulin / KIF14 / Kinesin-3
Biological speciesMus musculus (house mouse) / Bos taurus (domestic cattle)
Methodhelical reconstruction / cryo EM / Resolution: 15.5 Å
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.
History
DepositionMar 20, 2014-
Header (metadata) releaseApr 2, 2014-
Map releaseNov 19, 2014-
UpdateNov 19, 2014-
Current statusNov 19, 2014Processing site: PDBe / Status: Released

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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

emd-2609-Kif...

Downloads & links

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Map

FileDownload / File: emd_2609.map.gz / Format: CCP4 / Size: 918.9 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationkinesin KIF14 mtor domain micerotubule complex
Projections & slices

Image control

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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.01
Minimum - Maximum-0.14100054 - 0.16273578
Average (Standard dev.)0.00518579 (±0.04541813)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin14855148
Dimensions615868
Spacing615868
CellA: 116.0 Å / B: 122.0 Å / C: 136.0 Å
α=β=γ: 90.0 °

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
Components
  • Sample: Kinesin KIF14 motor domain microtubule complex
  • Protein or peptide: Kinesin KIF14 motor domain
  • Protein or peptide: Tubulin

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Supramolecule #1000: Kinesin KIF14 motor domain microtubule complex

SupramoleculeName: Kinesin KIF14 motor domain microtubule complex / type: sample / ID: 1000 / Number unique components: 2

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Macromolecule #1: Kinesin KIF14 motor domain

MacromoleculeName: Kinesin KIF14 motor domain / type: protein_or_peptide / ID: 1 / Recombinant expression: Yes
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #2: Tubulin

MacromoleculeName: Tubulin / type: protein_or_peptide / ID: 2 / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Bos taurus (domestic cattle)

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK I

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Electron microscopy

MicroscopeFEI TECNAI 20
DateNov 25, 2013
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Number real images: 30
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN

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Image processing

DetailsInitial 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.
Final reconstructionApplied symmetry - Helical parameters - Δz: 5.40237 Å
Applied symmetry - Helical parameters - Δ&Phi: 168.08788 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 15.5 Å / Resolution method: OTHER
Software - Name: SUPRIM, PHOELIX, IHRSR, SPIDER, CTFFIND3, CUSTOM, (emglue.py)
CTF correctionDetails: Each Particle

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Atomic model buiding 1

Initial modelPDB ID:

4ozq

SoftwareName: Chimera
DetailsThe 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.
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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Atomic model buiding 2

Initial modelPDB ID:

1jff

RefinementSpace: REAL / Protocol: RIGID BODY FIT

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