[English] 日本語
Yorodumi
- EMDB-5565: CS-tubulin Kinesin-13 Microtubule complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-5565
TitleCS-tubulin Kinesin-13 Microtubule complex
Map dataReconstruction of the kinesin-13 KLP10A head domain in complex with CS-tubulin and a microtubule
Sample
  • Sample: kinesin-13 KLP10A head domain in complex with CS-tubulin and a microtubule
  • Protein or peptide: KLP10A
  • Protein or peptide: Tubulin alpha-1A chain
  • Protein or peptide: Tubulin beta-2B chain
Keywordstubulin / microtubule / depolymerase / depolymerization / kinI / kinesin-13 / kinesin
Function / homology
Function and homology information


establishment of mitotic spindle asymmetry / establishment of meiotic spindle orientation / cortical microtubule / plus-end specific microtubule depolymerization / asymmetric protein localization involved in cell fate determination / meiotic spindle pole / mitotic spindle astral microtubule / COPI-dependent Golgi-to-ER retrograde traffic / Kinesins / centriole assembly ...establishment of mitotic spindle asymmetry / establishment of meiotic spindle orientation / cortical microtubule / plus-end specific microtubule depolymerization / asymmetric protein localization involved in cell fate determination / meiotic spindle pole / mitotic spindle astral microtubule / COPI-dependent Golgi-to-ER retrograde traffic / Kinesins / centriole assembly / mitotic chromosome movement towards spindle pole / kinetochore microtubule / meiotic spindle organization / spindle assembly involved in female meiosis I / non-motile cilium assembly / plus-end-directed microtubule motor activity / meiotic spindle / positive regulation of axon guidance / microtubule depolymerization / microtubule motor activity / spindle organization / kinesin complex / microtubule-based movement / mitotic spindle pole / cytoskeletal motor activity / centrosome duplication / microtubule-based process / chromosome, centromeric region / mitotic spindle organization / structural constituent of cytoskeleton / microtubule cytoskeleton organization / spindle pole / spindle / microtubule cytoskeleton / mitotic cell cycle / nervous system development / microtubule binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / protein heterodimerization activity / cell division / GTPase activity / centrosome / GTP binding / ATP hydrolysis activity / ATP binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Kinesin-like protein KIF2A-like, N-terminal / Kinesin-like protein / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Kinesin motor domain / Kinesin motor domain superfamily / Alpha tubulin ...Kinesin-like protein KIF2A-like, N-terminal / Kinesin-like protein / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Kinesin motor domain / Kinesin motor domain superfamily / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Tubulin alpha-1B chain / Tubulin beta-2B chain / Kinesin-like protein Klp10A
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly) / Bos taurus (cattle)
Methodhelical reconstruction / cryo EM / Resolution: 10.8 Å
AuthorsAsenjo AB / Chatterjee C / Tan D / DePaoli V / Rice WJ / Diaz-Avalos R / Silvestry M / Sosa H
CitationJournal: Cell Rep / Year: 2013
Title: Structural model for tubulin recognition and deformation by kinesin-13 microtubule depolymerases.
Authors: Ana B Asenjo / Chandrima Chatterjee / Dongyan Tan / Vania DePaoli / William J Rice / Ruben Diaz-Avalos / Mariena Silvestry / Hernando Sosa /
Abstract: To elucidate the structural basis of the mechanism of microtubule depolymerization by kinesin-13s, we analyzed complexes of tubulin and the Drosophila melanogaster kinesin-13 KLP10A by electron ...To elucidate the structural basis of the mechanism of microtubule depolymerization by kinesin-13s, we analyzed complexes of tubulin and the Drosophila melanogaster kinesin-13 KLP10A by electron microscopy (EM) and fluorescence polarization microscopy. We report a nanometer-resolution (1.1 nm) cryo-EM three-dimensional structure of the KLP10A head domain (KLP10AHD) bound to curved tubulin. We found that binding of KLP10AHD induces a distinct tubulin configuration with displacement (shear) between tubulin subunits in addition to curvature. In this configuration, the kinesin-binding site differs from that in straight tubulin, providing an explanation for the distinct interaction modes of kinesin-13s with the microtubule lattice or its ends. The KLP10AHD-tubulin interface comprises three areas of interaction, suggesting a crossbow-type tubulin-bending mechanism. These areas include the kinesin-13 family conserved KVD residues, and as predicted from the crossbow model, mutating these residues changes the orientation and mobility of KLP10AHDs interacting with the microtubule.
History
DepositionJan 9, 2013-
Header (metadata) releaseFeb 20, 2013-
Map releaseMar 6, 2013-
UpdateApr 10, 2013-
Current statusApr 10, 2013Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.015
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-3j2u
  • Surface level: 0.015
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3j2u
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5565_1.jpg

Downloads & links

-
Map

FileDownload / File: emd_5565.map.gz / Format: CCP4 / Size: 25.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of the kinesin-13 KLP10A head domain in complex with CS-tubulin and a microtubule
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2 Å/pix.
x 80 pix.
= 160. Å		2 Å/pix.
x 290 pix.
= 580. Å		2 Å/pix.
x 290 pix.
= 580. 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 EMDB: 0.015 / Movie #1: 0.015
Minimum - Maximum-0.12360548 - 0.15922026
Average (Standard dev.)0.00000776 (±0.02484056)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions29029080
Spacing29029080
CellA: 580.0 Å / B: 580.0 Å / C: 160.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z222
M x/y/z29029080
origin x/y/z0.0000.0000.000
length x/y/z580.000580.000160.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-5029166
NX/NY/NZ106122134
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS29029080
D min/max/mean-0.1240.1590.000

-
Supplemental data

-
Sample components

-
Entire : kinesin-13 KLP10A head domain in complex with CS-tubulin and a mi...

EntireName: kinesin-13 KLP10A head domain in complex with CS-tubulin and a microtubule
Components
  • Sample: kinesin-13 KLP10A head domain in complex with CS-tubulin and a microtubule
  • Protein or peptide: KLP10A
  • Protein or peptide: Tubulin alpha-1A chain
  • Protein or peptide: Tubulin beta-2B chain

-
Supramolecule #1000: kinesin-13 KLP10A head domain in complex with CS-tubulin and a mi...

SupramoleculeName: kinesin-13 KLP10A head domain in complex with CS-tubulin and a microtubule
type: sample / ID: 1000 / Oligomeric state: Helical / Number unique components: 2

-
Macromolecule #1: KLP10A

MacromoleculeName: KLP10A / type: protein_or_peptide / ID: 1 / Name.synonym: kinesin-13, kinI / Details: KLP10A head domain / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Drosophila melanogaster (fruit fly) / synonym: Fruit fly / Location in cell: cytoplasm
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceUniProtKB: Kinesin-like protein Klp10A

-
Macromolecule #2: Tubulin alpha-1A chain

MacromoleculeName: Tubulin alpha-1A chain / type: protein_or_peptide / ID: 2 / Details: Dimer with Tubulin beta-2B chain / Oligomeric state: helical multimer / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Bos taurus (cattle) / synonym: bovine / Tissue: brain
SequenceUniProtKB: Tubulin alpha-1B chain

-
Macromolecule #3: Tubulin beta-2B chain

MacromoleculeName: Tubulin beta-2B chain / type: protein_or_peptide / ID: 3 / Details: Dimer with Tubulin alpha-1A chain / Oligomeric state: helical multimer / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Bos taurus (cattle) / synonym: bovine / Tissue: brain
SequenceUniProtKB: Tubulin beta-2B chain

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

-
Sample preparation

VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK I

-
Electron microscopy #1

Microscopy ID1
MicroscopeJEOL 3200FSC
DateMay 1, 2012
Image recordingDigitization - Scanner: OTHER
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: JEOL

-
Electron microscopy #2

Microscopy ID2
MicroscopeFEI TECNAI F20
DateMay 1, 2012
Image recordingDigitization - Scanner: OTHER
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder: Gatan 626 / Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

-
Image processing

DetailsCustom single particle alignment method based on IHRSR
Final reconstructionApplied symmetry - Helical parameters - Δz: 5.55267 Å
Applied symmetry - Helical parameters - Δ&Phi: 168.08743 °
Resolution.type: BY AUTHOR / Resolution: 10.8 Å / Resolution method: OTHER / Software - Name: Spider, IHRSR, CTFFIND3, Custom
CTF correctionDetails: Each particle

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more