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- EMDB-9638: 4R-MAP4, kinesin-1, and microtubule complex -

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Basic information

Entry
Database: EMDB / ID: EMD-9638
Title4R-MAP4, kinesin-1, and microtubule complex
Map data4R-MAP4%u2013kinesin-1%u2013microtubule complex
Sample
  • Complex: Microtubule-Kinesin1-4R-MAP4 complex
Biological speciesBos taurus (cattle)
Methodhelical reconstruction / cryo EM / Resolution: 7.35 Å
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.
History
DepositionAug 28, 2018-
Header (metadata) releaseOct 10, 2018-
Map releaseOct 10, 2018-
UpdateDec 26, 2018-
Current statusDec 26, 2018Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 4
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9638.png

Downloads & links

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Map

FileDownload / File: emd_9638.map.gz / Format: CCP4 / Size: 14.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation4R-MAP4%u2013kinesin-1%u2013microtubule complex
Voxel sizeX=Y=Z: 1.284 Å
Density
Contour LevelBy AUTHOR: 3. / Movie #1: 4
Minimum - Maximum-7.562476 - 19.190951999999999
Average (Standard dev.)1.2781348 (±3.3270278)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-120-1000
Dimensions155129193
Spacing129155193
CellA: 165.636 Å / B: 199.02 Å / C: 247.81201 Å
α=β=γ: 90.0 °

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
MAP C/R/S123
start NC/NR/NS-100-1200
NC/NR/NS129155193
D min/max/mean-7.56219.1911.278

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Supplemental data

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Sample components

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Entire : Microtubule-Kinesin1-4R-MAP4 complex

EntireName: Microtubule-Kinesin1-4R-MAP4 complex
Components
  • Complex: Microtubule-Kinesin1-4R-MAP4 complex

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Supramolecule #1: Microtubule-Kinesin1-4R-MAP4 complex

SupramoleculeName: Microtubule-Kinesin1-4R-MAP4 complex / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Bos taurus (cattle)
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: BL-21(DE3)pLysS / Recombinant plasmid: pET21d

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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 / Details: 100mM PIPES-KOH at pH 6.8, 1mM MgCl2, 1mM EGTA
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 300 K / Instrument: FEI VITROBOT MARK IV / Details: Blot time 5sec, Blot Force 20.

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Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 30.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 78000
Sample stageSpecimen holder model: OTHER / Cooling holder cryogen: NITROGEN
DetailsAlignment procedure by FEI User Interface Software. Not determined the residual tilt value.
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Frames/image: 1-34 / Number grids imaged: 1 / Average exposure time: 2.0 sec. / Average electron dose: 55.0 e/Å2
Details: Images were collected in movie-mode at 17 frames per second by using Falcon Hack developed by Greg McMullan
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 3)
Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Helical parameters - Δz: 8.7 Å
Applied symmetry - Helical parameters - Δ&Phi: -25.76 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 7.35 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 77616

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