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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
KeywordsKinesin / Micotubule / Tubulin / KIF14 / Kinesin-3
SampleKinesin KIF14 motor domain microtubule complex
SourceMus musculus / mammal / ハツカネズミ, はつかねずみ /
Bos taurus / mammal / ウシ /
Map datakinesin KIF14 mtor domain micerotubule complex
Methodhelical reconstruction, at 15.5 Å resolution
AuthorsArora K / Talje L / Asenjo AB / Andersen P / Atchia K / Joshi M / Sosa H / Allingham JS / Kwok BH
CitationJ. Mol. Biol., 2014, 426, 2997-3015

J. Mol. Biol., 2014, 426, 2997-3015 Yorodumi Papers
KIF14 binds tightly to microtubules and adopts a rigor-like conformation.
Kritica Arora / Lama Talje / Ana B Asenjo / Parker Andersen / Kaleem Atchia / Monika Joshi / Hernando Sosa / John S Allingham / Benjamin H Kwok

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
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  • Surface view colored by cylindrical radius
  • Surface level: 0.01
  • Imaged by UCSF CHIMERA
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Supplemental images

Downloads & links

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Map

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

Image control

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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

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Images are generated by Spider package.

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 / mammal / ハツカネズミ, はつかねずみ /
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #2: protein, Tubulin

ProteinName: Tubulin / Recombinant expression: No
SourceSpecies: Bos taurus / mammal / ウシ /

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Experimental details

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Sample preparation

Specimen statehelical array
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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