[English] 日本語
Yorodumi
- EMDB-8408: Cryo-EM reconstruction of the yeast kinesin-5, Cin8, bound to GDP... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-8408
TitleCryo-EM reconstruction of the yeast kinesin-5, Cin8, bound to GDP-taxol microtubules in ADP-AlFx state
Map data3D helical reconstruction of Cin8 motor domain in ADP-AlFx state bound to microtubule using cryo-EM
Sample
  • Complex: Microtubule-bound kinesin-5 Cin8 in ADP-AlFx state
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodhelical reconstruction / cryo EM / Resolution: 7.3 Å
AuthorsCha HK
CitationJournal: J Biol Chem / Year: 2017
Title: The yeast kinesin-5 Cin8 interacts with the microtubule in a noncanonical manner.
Authors: Kayla M Bell / Hyo Keun Cha / Charles V Sindelar / Jared C Cochran /
Abstract: Kinesin motors play central roles in establishing and maintaining the mitotic spindle during cell division. Unlike most other kinesins, Cin8, a kinesin-5 motor in can move bidirectionally along ...Kinesin motors play central roles in establishing and maintaining the mitotic spindle during cell division. Unlike most other kinesins, Cin8, a kinesin-5 motor in can move bidirectionally along microtubules, switching directionality according to biochemical conditions, a behavior that remains largely unexplained. To this end, we used biochemical rate and equilibrium constant measurements as well as cryo-electron microscopy methodologies to investigate the microtubule interactions of the Cin8 motor domain. These experiments unexpectedly revealed that, whereas Cin8 ATPase kinetics fell within measured ranges for kinesins (especially kinesin-5 proteins), approximately four motors can bind each αβ-tubulin dimer within the microtubule lattice. This result contrasted with those observations on other known kinesins, which can bind only a single "canonical" site per tubulin dimer. Competition assays with human kinesin-5 (Eg5) only partially abrogated this behavior, indicating that Cin8 binds microtubules not only at the canonical site, but also one or more separate ("noncanonical") sites. Moreover, we found that deleting the large, class-specific insert in the microtubule-binding loop 8 reverts Cin8 to one motor per αβ-tubulin in the microtubule. The novel microtubule-binding mode of Cin8 identified here provides a potential explanation for Cin8 clustering along microtubules and potentially may contribute to the mechanism for direction reversal.
History
DepositionOct 1, 2016-
Header (metadata) releaseOct 12, 2016-
Map releaseJul 26, 2017-
UpdateSep 13, 2017-
Current statusSep 13, 2017Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0957
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0957
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0957
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8408.png

Downloads & links

-
Map

FileDownload / File: emd_8408.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3D helical reconstruction of Cin8 motor domain in ADP-AlFx state bound to microtubule using cryo-EM
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.49 Å/pix.
x 280 pix.
= 698.326 Å		2.49 Å/pix.
x 280 pix.
= 698.326 Å		2.49 Å/pix.
x 280 pix.
= 698.326 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.49402 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0957 / Movie #1: 0.0957
Minimum - Maximum0. - 0.21301804
Average (Standard dev.)0.0074020033 (±0.024142148)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-140-140-140
Dimensions280280280
Spacing280280280
CellA=B=C: 698.3256 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.49402142857142.49402142857142.4940214285714
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z698.326698.326698.326
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-140-140-140
NC/NR/NS280280280
D min/max/mean0.0000.2130.007

-
Supplemental data

-
Sample components

-
Entire : Microtubule-bound kinesin-5 Cin8 in ADP-AlFx state

EntireName: Microtubule-bound kinesin-5 Cin8 in ADP-AlFx state
Components
  • Complex: Microtubule-bound kinesin-5 Cin8 in ADP-AlFx state

-
Supramolecule #1: Microtubule-bound kinesin-5 Cin8 in ADP-AlFx state

SupramoleculeName: Microtubule-bound kinesin-5 Cin8 in ADP-AlFx state / type: complex / ID: 1 / Parent: 0
Details: Cin8-his monomer (residues 70-535) Taxol-stabilized microtubules
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant cell: B834(DE3) / Recombinant plasmid: pET16b

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

-
Sample preparation

BufferpH: 6.8
Component:
ConcentrationFormulaName
25.0 mMPIPESpiperazine-N,N-bis
25.0 mMNaClSodium chloridesodium chloride
2.0 mMMgCl2magnesium chloride
1.0 mMEGTAEthylene glycol-bis(2-aminoethylether)-N,N,N,N-tetraacetic acid

Details: adjusted to pH 6.8 with KOH
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER

-
Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 1.71 e/Å2
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

-
Image processing

CTF correctionSoftware - Name: CTFFIND3
Final angle assignmentType: NOT APPLICABLE / Software - Name: SPIDER
Final reconstructionApplied symmetry - Helical parameters - Δz: 9.455 Å
Applied symmetry - Helical parameters - Δ&Phi: -25.77 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 7.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: FREALIGN / Number images used: 2282
FSC plot (resolution estimation)

+
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