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- EMDB-9637: 5R-MAP4, kinesin-1, and microtubule complex -

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Basic information

Entry
Database: EMDB / ID: 9637
Title5R-MAP4, kinesin-1, and microtubule complex
Map data
SampleMicrotubule-Kinesin-1-5R-MAP4 complex:
SourceBos taurus (cattle)
Methodhelical reconstruction / cryo EM / 7.29 Å resolution
AuthorsShigematsu H / Imasaki T / Doki C / Sumi T / Aoki M / Uchikubo-Kamo T / Sakamoto A / Tokuraku K / Shirouzu M / Nitta R
CitationJournal: J. Cell Biol. / Year: 2018
Title: Structural insight into microtubule stabilization and kinesin inhibition by Tau family MAPs.
Authors: Hideki Shigematsu / Tsuyoshi Imasaki / Chihiro Doki / Takuya Sumi / Mari Aoki / Tomomi Uchikubo-Kamo / Ayako Sakamoto / Kiyotaka Tokuraku / Mikako Shirouzu / Ryo Nitta
Abstract: The Tau family microtubule-associated proteins (MAPs) promote microtubule stabilization and regulate microtubule-based motility. They share the C-terminal microtubule-binding domain, which includes ...The Tau family microtubule-associated proteins (MAPs) promote microtubule stabilization and regulate microtubule-based motility. They share the C-terminal microtubule-binding domain, which includes three to five tubulin-binding repeats. Different numbers of repeats formed by alternative splicing have distinct effects on the activities of these proteins, and the distribution of these variants regulates fundamental physiological phenomena in cells. In this study, using cryo-EM, we visualized the MAP4 microtubule complex with the molecular motor kinesin-1. MAP4 bound to the C-terminal domains of tubulins along the protofilaments stabilizes the longitudinal contacts of the microtubule. The strongest bond of MAP4 was found around the intertubulin-dimer interface such that MAP4 coexists on the microtubule with kinesin-1 bound to the intratubulin-dimer interface as well. MAP4, consisting of five repeats, further folds and accumulates above the intertubulin-dimer interface, interfering with kinesin-1 movement. Therefore, these cryo-EM studies reveal new insight into the structural basis of microtubule stabilization and inhibition of kinesin motility by the Tau family MAPs.
DateDeposition: Aug 28, 2018 / Header (metadata) release: Oct 10, 2018 / Map release: Oct 10, 2018 / Last update: Oct 17, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 5
  • 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_9637.map.gz (map file in CCP4 format, 15437 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
193 pix
1.28 Å/pix.
= 247.812 Å
155 pix
1.28 Å/pix.
= 199.02 Å
129 pix
1.28 Å/pix.
= 165.636 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.284 Å
Density
Contour Level:3.0 (by author), 5 (movie #1):
Minimum - Maximum-8.954687 - 21.335326999999999
Average (Standard dev.)1.0217452 (3.3864448)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions155129193
Origin-120.0-100.00.0
Limit34.028.0192.0
Spacing129155193
CellA: 165.636 Å / B: 199.02 Å / C: 247.81201 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.2841.2841.284
M x/y/z129155193
origin x/y/z0.0000.0000.000
length x/y/z165.636199.020247.812
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS-100-1200
NC/NR/NS129155193
D min/max/mean-8.95521.3351.022

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Supplemental data

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Sample components

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Entire Microtubule-Kinesin-1-5R-MAP4 complex

EntireName: Microtubule-Kinesin-1-5R-MAP4 complex / Number of components: 1

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Component #1: protein, Microtubule-Kinesin-1-5R-MAP4 complex

ProteinName: Microtubule-Kinesin-1-5R-MAP4 complex / Recombinant expression: No
SourceSpecies: Bos taurus (cattle)
Source (engineered)Expression System: Escherichia coli (E. coli) / Vector: pET21d / Strain: BL21(DE3)pLysS

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Experimental details

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Sample preparation

SpecimenSpecimen state: filament / Method: cryo EM
Helical parametersAxial symmetry: C1 (asymmetric) / Delta z: 8.7 Å / Delta phi: -25.76 deg.
Sample solutionBuffer solution: 100 mM PIPES-KOH at pH 6.8, 1 mM MgCl2, 1 mM EGTA
pH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 300 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI ARCTICA
Details: Alignment procedure by FEI User Interface Software. Not determined the residual tilt value.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 55 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 78000.0 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1500.0 - 2500.0 nm
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

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Image processing

ProcessingMethod: helical reconstruction
3D reconstructionResolution: 7.29 Å / Resolution method: FSC 0.143 CUT-OFF

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