[English] 日本語
Yorodumi
- EMDB-5027: Kinesin13-Microtubule Ring Complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-5027
TitleKinesin13-Microtubule Ring Complex
Map dataKinesin 13-Microtubule Ring Complex
Sample
  • Sample: Kinesin13-Microtubule Ring Complex
  • Protein or peptide: KLP10a
  • Protein or peptide: alpha-tubulin
  • Protein or peptide: beta-tubulinTubulin
KeywordsKinesin / Kinesin-13 / microtubule / tubulin / depolymerization / Kin-I / M-Kinesin / cytoskeleton
Function / homology
Function and homology information


regulation of chromosome segregation / metaphase chromosome alignment / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / establishment or maintenance of microtubule cytoskeleton polarity / Kinesins / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / RHO GTPases Activate Formins / COPI-dependent Golgi-to-ER retrograde traffic ...regulation of chromosome segregation / metaphase chromosome alignment / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / establishment or maintenance of microtubule cytoskeleton polarity / Kinesins / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / RHO GTPases Activate Formins / COPI-dependent Golgi-to-ER retrograde traffic / Separation of Sister Chromatids / microtubule plus-end / attachment of mitotic spindle microtubules to kinetochore / MHC class II antigen presentation / microtubule plus-end binding / microtubule depolymerization / tubulin complex / kinesin complex / microtubule motor activity / mitotic metaphase chromosome alignment / microtubule-based movement / chromosome, centromeric region / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / spindle / microtubule cytoskeleton organization / kinetochore / microtubule cytoskeleton / mitotic cell cycle / microtubule binding / microtubule / hydrolase activity / cell division / GTPase activity / centrosome / GTP binding / ATP hydrolysis activity / ATP binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Kinesin-like protein / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Kinesin motor domain superfamily / Tubulin-beta mRNA autoregulation signal. / Alpha tubulin ...Kinesin-like protein / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Kinesin motor domain superfamily / Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / Alpha tubulin / Beta tubulin, autoregulation binding site / Beta tubulin / 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-1A chain / Tubulin beta chain / Tubulin alpha-1D chain / Kinesin-like protein KIF2C
Similarity search - Component
Methodhelical reconstruction / cryo EM / Resolution: 28.0 Å
AuthorsTan D / Rice WJ / Sosa H
CitationJournal: Structure / Year: 2008
Title: Structure of the kinesin13-microtubule ring complex.
Authors: Dongyan Tan / William J Rice / Hernando Sosa /
Abstract: To investigate the mechanism of kinesin13-induced microtubule depolymerization, we have calculated a three-dimensional (3D) map of the kinesin13-microtubule ring complex, using cryo-electron ...To investigate the mechanism of kinesin13-induced microtubule depolymerization, we have calculated a three-dimensional (3D) map of the kinesin13-microtubule ring complex, using cryo-electron microscopy (cryo-EM) and image analysis. An atomic model of the complex was produced by docking the crystal structures of tubulin and a kinesin13 motor domain (MD) into the 3D map. The model reveals a snapshot of the depolymerization mechanism by providing a 3D view of the complex formed between the kinesin13 MD and a curved tubulin protofilament (pf). It suggests that contacts mediated by kinesin13 class-specific residues in the putative microtubule-binding site stabilize intra-dimer tubulin curvature. In addition, a tubulin-binding site on the kinesin13 MD was identified. Mutations at this class-conserved site selectively disrupt the formation of microtubule-associated ring complexes.
History
DepositionAug 29, 2008-
Header (metadata) releaseDec 17, 2008-
Map releaseMay 5, 2009-
UpdateApr 2, 2014-
Current statusApr 2, 2014Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 14
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 14
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-3edl
  • Surface level: 14
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3edl
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5027_1.tif

Downloads & links

-
Map

FileDownload / File: emd_5027.map.gz / Format: CCP4 / Size: 1.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationKinesin 13-Microtubule Ring Complex
Voxel sizeX=Y=Z: 6 Å
Density
Contour LevelBy AUTHOR: 11.1 / Movie #1: 14
Minimum - Maximum-48.0 - 55.0
Average (Standard dev.)0.56261343 (±12.836534500000001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions10110141
Spacing10110141
CellA: 606.0 Å / B: 606.0 Å / C: 246.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z666
M x/y/z10110141
origin x/y/z0.0000.0000.000
length x/y/z606.000606.000246.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-127-127-127
NX/NY/NZ255255255
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS10110141
D min/max/mean-48.00055.0000.563

-
Supplemental data

-
Sample components

-
Entire : Kinesin13-Microtubule Ring Complex

EntireName: Kinesin13-Microtubule Ring Complex
Components
  • Sample: Kinesin13-Microtubule Ring Complex
  • Protein or peptide: KLP10a
  • Protein or peptide: alpha-tubulin
  • Protein or peptide: beta-tubulinTubulin

-
Supramolecule #1000: Kinesin13-Microtubule Ring Complex

SupramoleculeName: Kinesin13-Microtubule Ring Complex / type: sample / ID: 1000 / Number unique components: 3
Molecular weightExperimental: 250 KDa / Theoretical: 250 KDa / Method: SDS-PAGE

-
Macromolecule #1: KLP10a

MacromoleculeName: KLP10a / type: protein_or_peptide / ID: 1 / Name.synonym: Kinesin-13 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: Yes
Source (natural)Cell: BL21 / Location in cell: cytosol
Molecular weightExperimental: 400 KDa / Theoretical: 400 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pRSET B

-
Macromolecule #2: alpha-tubulin

MacromoleculeName: alpha-tubulin / type: protein_or_peptide / ID: 2 / Name.synonym: tubulin / Number of copies: 2 / Oligomeric state: Heterodimer / Recombinant expression: No / Database: NCBI
Source (natural)Tissue: Bos taurus Brain
Molecular weightExperimental: 550 KDa
SequenceGO: tubulin complex / InterPro: Alpha tubulin

-
Macromolecule #3: beta-tubulin

MacromoleculeName: beta-tubulin / type: protein_or_peptide / ID: 3 / Name.synonym: tubulin / Number of copies: 2 / Oligomeric state: Hterodimer / Recombinant expression: No / Database: NCBI
Source (natural)Tissue: Brain
Molecular weightExperimental: 550 KDa
SequenceGO: tubulin complex / InterPro: Beta tubulin

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

-
Sample preparation

Concentration0.6 mg/mL
BufferpH: 6.8
Details: 80 mM Pipes, pH 6.8, 2 mM MgCl2, 1 mM EGTA, 2 mM AMP-PNP, 0.02 mM taxol
GridDetails: Quantifoil grids
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: OTHER / Details: Vitrification instrument: VitroBot
Method: Blot for 2 seconds, Blot Offset (mm) -2, Plunge Time 1 sec, Wait Time 0 sec

-
Electron microscopy #1

MicroscopeFEI TECNAI 20
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Side entry liquid nitrogen-cooled cryo specimen holder
Specimen holder model: GATAN LIQUID NITROGEN
Microscopy ID1
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 12.5 µm / Number real images: 5 / Average electron dose: 9 e/Å2 / Bits/pixel: 16

-
Electron microscopy #2

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 50000
Sample stageSpecimen holder: Side entry liquid nitrogen-cooled cryo specimen holder
Specimen holder model: GATAN LIQUID NITROGEN
Microscopy ID2
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 12.5 µm / Number real images: 5 / Average electron dose: 9 e/Å2 / Bits/pixel: 16
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

-
Image processing

CTF correctionDetails: Each Particle
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 28.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: MRC, SUPRIM, Phoelix, Other
Details: Final map is the averaged near and far layer line data from 5 filaments (10 datasets, 3296 asymmetric units)

-
Atomic model buiding 1

Initial modelPDB ID:

1v8k


Chain - Chain ID: A
SoftwareName: COLORES
DetailsPDBEntryID_givenInChain. Protocol: Rigid-Body
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-3edl:
Kinesin13-Microtubule Ring complex

-
Atomic model buiding 2

Initial modelPDB ID:

1jff

SoftwareName: COLORES
DetailsProtocol: Rigid Body
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-3edl:
Kinesin13-Microtubule Ring complex

-
Atomic model buiding 3

Initial modelPDB ID:

1sa0

SoftwareName: COLORES
DetailsProtocol: Rigid Body
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-3edl:
Kinesin13-Microtubule Ring complex

+
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