[English] 日本語
Yorodumi
- EMDB-8061: Structural basis of backwards motion in kinesin-14: plus-end dire... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-8061
TitleStructural basis of backwards motion in kinesin-14: plus-end directed nKn669 in the nucleotide-free state
Map dataNone
Sample
  • Complex: Plus-end directed Ncd chimera nKn669 in the nucleotide-free state complexed with GDP-taxol microtubule
    • Complex: Tubulin alpha-1B chain
      • Protein or peptide: Tubulin alpha-1B chain
    • Complex: Tubulin beta-2B chain
      • Protein or peptide: Tubulin beta-2B chain
    • Complex: Protein claret segregational,Plus-end directed kinesin-1/kinesin-14,Protein claret segregational
      • Protein or peptide: Protein claret segregational,Protein claret segregational,Plus-end directed kinesin-1/kinesin-14,Protein claret segregational,Protein claret segregational
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: TAXOLPaclitaxel
Keywordskinesin / kinesin-14 / microtubule / ATPase / STRUCTURAL PROTEIN-MOTOR PROTEIN complex
Function / homology
Function and homology information


minus-end directed microtubule sliding / distributive segregation / regulation of mitotic spindle elongation / meiotic spindle assembly / mitotic spindle elongation / mitotic spindle microtubule / meiotic spindle organization / spindle assembly involved in female meiosis / minus-end-directed microtubule motor activity / regulation of mitotic spindle assembly ...minus-end directed microtubule sliding / distributive segregation / regulation of mitotic spindle elongation / meiotic spindle assembly / mitotic spindle elongation / mitotic spindle microtubule / meiotic spindle organization / spindle assembly involved in female meiosis / minus-end-directed microtubule motor activity / regulation of mitotic spindle assembly / microtubule bundle formation / meiotic spindle / mitotic centrosome separation / positive regulation of axon guidance / spindle organization / mitotic spindle assembly / mRNA transport / cytoplasmic microtubule / microtubule-based process / cellular response to interleukin-4 / mitotic spindle organization / chromosome segregation / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / spindle / microtubule cytoskeleton organization / microtubule cytoskeleton / double-stranded RNA binding / mitotic cell cycle / nervous system development / microtubule binding / microtubule / hydrolase activity / protein heterodimerization activity / cell division / GTPase activity / centrosome / ubiquitin protein ligase binding / GTP binding / protein homodimerization activity / ATP binding / metal ion binding / nucleus / cytosol / 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 / 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
Protein claret segregational / Tubulin alpha-1B chain / Tubulin beta-2B chain
Similarity search - Component
Biological speciesBos taurus (cattle) / Drosophila melanogaster (fruit fly)
Methodhelical reconstruction / cryo EM / Resolution: 5.8 Å
AuthorsShigematsu H / Yokoyama T / Kikkawa M / Shirouzu M / Nitta R
CitationJournal: Structure / Year: 2016
Title: Structural Basis of Backwards Motion in Kinesin-1-Kinesin-14 Chimera: Implication for Kinesin-14 Motility.
Authors: Masahiko Yamagishi / Hideki Shigematsu / Takeshi Yokoyama / Masahide Kikkawa / Mitsuhiro Sugawa / Mari Aoki / Mikako Shirouzu / Junichiro Yajima / Ryo Nitta /
Abstract: Kinesin-14 is a unique minus-end-directed microtubule-based motor. A swinging motion of a class-specific N-terminal neck helix has been proposed to produce minus-end directionality. However, it is ...Kinesin-14 is a unique minus-end-directed microtubule-based motor. A swinging motion of a class-specific N-terminal neck helix has been proposed to produce minus-end directionality. However, it is unclear how swinging of the neck helix is driven by ATP hydrolysis utilizing the highly conserved catalytic core among all kinesins. Here, using a motility assay, we show that in addition to the neck helix, the conserved five residues at the C-terminal region in kinesin-14, namely the neck mimic, are necessary to give kinesin-1 an ability to reverse its directionality toward the minus end of microtubules. Our structural analyses further demonstrate that the C-terminal neck mimic, in cooperation with conformational changes in the catalytic core during ATP binding, forms a kinesin-14 bundle with the N-terminal neck helix to swing toward the minus end of microtubules. Thus, the neck mimic plays a crucial role in coupling the chemical ATPase reaction with the mechanical cycle to produce the minus-end-directed motility of kinesin-14.
History
DepositionApr 5, 2016-
Header (metadata) releaseAug 10, 2016-
Map releaseAug 10, 2016-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4.6
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 4.6
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-5hnz
  • Surface level: 4.6
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5hnz
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8061.png

Downloads & links

-
Map

FileDownload / File: emd_8061.map.gz / Format: CCP4 / Size: 12 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNone
Voxel sizeX=Y=Z: 1.284 Å
Density
Contour LevelBy AUTHOR: 4.6 / Movie #1: 4.6
Minimum - Maximum-4.5824456 - 14.075746000000001
Average (Standard dev.)1.0623357 (±2.8839939)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin256256384
Dimensions128128192
Spacing128128192
CellA: 164.352 Å / B: 164.352 Å / C: 246.52802 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.2841.2841.284
M x/y/z128128192
origin x/y/z0.0000.0000.000
length x/y/z164.352164.352246.528
α/β/γ90.00090.00090.000
start NX/NY/NZ-38-19-20
NX/NY/NZ858082
MAP C/R/S123
start NC/NR/NS256256384
NC/NR/NS128128192
D min/max/mean-4.58214.0761.062

-
Supplemental data

-
Sample components

+
Entire : Plus-end directed Ncd chimera nKn669 in the nucleotide-free state...

EntireName: Plus-end directed Ncd chimera nKn669 in the nucleotide-free state complexed with GDP-taxol microtubule
Components
  • Complex: Plus-end directed Ncd chimera nKn669 in the nucleotide-free state complexed with GDP-taxol microtubule
    • Complex: Tubulin alpha-1B chain
      • Protein or peptide: Tubulin alpha-1B chain
    • Complex: Tubulin beta-2B chain
      • Protein or peptide: Tubulin beta-2B chain
    • Complex: Protein claret segregational,Plus-end directed kinesin-1/kinesin-14,Protein claret segregational
      • Protein or peptide: Protein claret segregational,Protein claret segregational,Plus-end directed kinesin-1/kinesin-14,Protein claret segregational,Protein claret segregational
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: TAXOLPaclitaxel

+
Supramolecule #1: Plus-end directed Ncd chimera nKn669 in the nucleotide-free state...

SupramoleculeName: Plus-end directed Ncd chimera nKn669 in the nucleotide-free state complexed with GDP-taxol microtubule
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

+
Supramolecule #2: Tubulin alpha-1B chain

SupramoleculeName: Tubulin alpha-1B chain / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1

+
Supramolecule #3: Tubulin beta-2B chain

SupramoleculeName: Tubulin beta-2B chain / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2

+
Supramolecule #4: Protein claret segregational,Plus-end directed kinesin-1/kinesin-...

SupramoleculeName: Protein claret segregational,Plus-end directed kinesin-1/kinesin-14,Protein claret segregational
type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3

+
Macromolecule #1: Tubulin alpha-1B chain

MacromoleculeName: Tubulin alpha-1B chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (cattle)
Molecular weightTheoretical: 50.107238 KDa
SequenceString: MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVDL EPTVIDEVRT GTYRQLFHP EQLITGKEDA ANNYARGHYT IGKEIIDLVL DRIRKLADQC TGLQGFSVFH SFGGGTGSGF TSLLMERLSV D YGKKSKLE ...String:
MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVDL EPTVIDEVRT GTYRQLFHP EQLITGKEDA ANNYARGHYT IGKEIIDLVL DRIRKLADQC TGLQGFSVFH SFGGGTGSGF TSLLMERLSV D YGKKSKLE FSIYPAPQVS TAVVEPYNSI LTTHTTLEHS DCAFMVDNEA IYDICRRNLD IERPTYTNLN RLIGQIVSSI TA SLRFDGA LNVDLTEFQT NLVPYPRGHF PLATYAPVIS AEKAYHEQLS VAEITNACFE PANQMVKCDP RHGKYMACCL LYR GDVVPK DVNAAIATIK TKRTIQFVDW CPTGFKVGIN YEPPTVVPGG DLAKVQRAVC MLSNTTAIAE AWARLDHKFD LMYA KRAFV HWYVGEGMEE GEFSEAREDM AALEKDYEEV GVDSVEGEGE EEGEEY

UniProtKB: Tubulin alpha-1B chain

+
Macromolecule #2: Tubulin beta-2B chain

MacromoleculeName: Tubulin beta-2B chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (cattle)
Molecular weightTheoretical: 49.90777 KDa
SequenceString: MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGSYHGDS DLQLERINVY YNEAAGNKYV PRAILVDLEP GTMDSVRSGP FGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV VRKESESCDC LQGFQLTHSL GGGTGSGMGT LLISKIREEY P DRIMNTFS ...String:
MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGSYHGDS DLQLERINVY YNEAAGNKYV PRAILVDLEP GTMDSVRSGP FGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV VRKESESCDC LQGFQLTHSL GGGTGSGMGT LLISKIREEY P DRIMNTFS VVPSPKVSDT VVEPYNATLS VHQLVENTDE TYCIDNEALY DICFRTLKLT TPTYGDLNHL VSATMSGVTT CL RFPGQLN ADLRKLAVNM VPFPRLHFFM PGFAPLTSRG SQQYRALTVP ELTQQMFDAK NMMAACDPRH GRYLTVAAVF RGR MSMKEV DEQMLNVQNK NSSYFVEWIP NNVKTAVCDI PPRGLKMSAT FIGNSTAIQE LFKRISEQFT AMFRRKAFLH WYTG EGMDE MEFTEAESNM NDLVSEYQQY QDATADEQGE FEEEEGEDEA

UniProtKB: Tubulin beta-2B chain

+
Macromolecule #3: Protein claret segregational,Protein claret segregational,Plus-en...

MacromoleculeName: Protein claret segregational,Protein claret segregational,Plus-end directed kinesin-1/kinesin-14,Protein claret segregational,Protein claret segregational
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 41.720418 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: KEQLFQSNME RKELHNTVMD LRGNIKVMCR FRPLNEAEIL RGDKFIPKFK GEETVVIQGK PYVFDRVLPP NTTQEQVYNA CAKQIVKDV LEGYNGTIFA YGQTSSGKTH TMEGKLHDPQ LMGIIPRIAH DIFDHIYSMD ENLEFAIKVS YFEIYLDKIR D LLDVSKTN ...String:
KEQLFQSNME RKELHNTVMD LRGNIKVMCR FRPLNEAEIL RGDKFIPKFK GEETVVIQGK PYVFDRVLPP NTTQEQVYNA CAKQIVKDV LEGYNGTIFA YGQTSSGKTH TMEGKLHDPQ LMGIIPRIAH DIFDHIYSMD ENLEFAIKVS YFEIYLDKIR D LLDVSKTN LAVHEDKNRV PYVKGCTERF VSSPEEVMDV IDEGKSNRHV AVTNMNEHSS RSHSIFLINI KQENVETEKK LS GKLYLVD LAGSEKVSKT GAEGAVLDEA KNINKSLSAL GNVISALAEG TTHVPYRDSK MTRILQDSLG GNCRTTIVIC CSP SVFNEA ETKSTLMFGQ RAKSCKMTKA KRNRYLNNSV ANSSTQSNNS GSFDK

UniProtKB: Protein claret segregational, Protein claret segregational

+
Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #5: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM / Guanosine triphosphate

+
Macromolecule #6: GUANOSINE-5'-DIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 1 / Formula: GDP
Molecular weightTheoretical: 443.201 Da
Chemical component information

ChemComp-GDP:
GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying molecule*YM / Guanosine diphosphate

+
Macromolecule #7: TAXOL

MacromoleculeName: TAXOL / type: ligand / ID: 7 / Number of copies: 1 / Formula: TA1
Molecular weightTheoretical: 853.906 Da
Chemical component information

ChemComp-TA1:
TAXOL / medication, chemotherapy*YM / Paclitaxel

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

-
Sample preparation

BufferpH: 6.8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TECNAI ARCTICA
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: FEI FALCON II (4k x 4k) / Average electron dose: 30.0 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: EMDB MAP
Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Helical parameters - Δz: 8.77999 Å
Applied symmetry - Helical parameters - Δ&Phi: -25.718312 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 5.8 Å / Resolution method: FSC 0.143 CUT-OFF / Details: High-resolution noise substitution was performed / Number images used: 203826

-
Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT
Output model

PDB-5hnz:
Structural basis of backwards motion in kinesin-14: plus-end directed nKn669 in the nucleotide-free state

+
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