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- EMDB-39669: Kinesin-14 with AMPPNP bound to 14 PF Microtubule -

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Basic information

Entry
Database: EMDB / ID: EMD-39669
TitleKinesin-14 with AMPPNP bound to 14 PF Microtubule
Map data
Sample
  • Complex: Kinesin-microtubule complex
    • Complex: Tubulin
      • Protein or peptide: Tubulin alpha-1B chain Q2XVP4
      • Protein or peptide: Tubulin beta-5B chain Q767L7
    • Complex: NCD
      • Protein or peptide: NCD
KeywordsKinesin Motor Proteins / Force Production / Power Stroke Fluctuations / Motor Spring-like Element / Reversed Motility / Mechanochemical Coupling / Mechanical States / CELL CYCLE
Function / homology
Function and homology information


minus-end directed microtubule sliding / distributive segregation / regulation of mitotic spindle elongation / meiotic spindle assembly / Regulation of PLK1 Activity at G2/M Transition / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / Recruitment of mitotic centrosome proteins and complexes ...minus-end directed microtubule sliding / distributive segregation / regulation of mitotic spindle elongation / meiotic spindle assembly / Regulation of PLK1 Activity at G2/M Transition / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / Recruitment of mitotic centrosome proteins and complexes / mitotic spindle elongation / odontoblast differentiation / mitotic spindle microtubule / meiotic spindle organization / Neutrophil degranulation / microtubule bundle formation / spindle assembly involved in female meiosis / regulation of mitotic spindle assembly / mitotic centrosome separation / meiotic spindle / Recruitment of NuMA to mitotic centrosomes / minus-end-directed microtubule motor activity / spindle organization / regulation of synapse organization / nuclear envelope lumen / MHC class I protein binding / mitotic spindle assembly / mRNA transport / intercellular bridge / spindle assembly / mitotic spindle organization / chromosome segregation / structural constituent of cytoskeleton / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / microtubule cytoskeleton organization / spindle / cytoplasmic ribonucleoprotein granule / mitotic spindle / mitotic cell cycle / cell body / microtubule binding / microtubule / hydrolase activity / cell division / GTPase activity / ubiquitin protein ligase binding / centrosome / 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. / Beta tubulin, autoregulation binding site ...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. / 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 beta chain
Similarity search - Component
Biological speciesSus scrofa (pig) / Drosophila melanogaster (fruit fly) / Drosophila melanogaster
Methodhelical reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsShibata S / Imasaki T / Shigematsu H / Endow SA / Nitta R
Funding support Japan, 4 items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJFR214K Japan
Japan Science and TechnologyJPMJMS2024 Japan
Japan Agency for Medical Research and Development (AMED)JP21gm1610003 Japan
Japan Society for the Promotion of Science (JSPS)22K06809 Japan
CitationJournal: bioRxiv / Year: 2024
Title: Structural transitions in kinesin minus-end directed microtubule motility.
Authors: Satoki Shibata / Matthew Y Wang / Tsuyoshi Imasaki / Hideki Shigematsu / Yuanyuan Wei / Chacko Jobichen / Hajime Hagio / J Sivaraman / Sharyn A Endow / Ryo Nitta /
Abstract: Kinesin motor proteins hydrolyze ATP to produce force for spindle assembly and vesicle transport, performing essential functions in cell division and motility, but the structural changes required for ...Kinesin motor proteins hydrolyze ATP to produce force for spindle assembly and vesicle transport, performing essential functions in cell division and motility, but the structural changes required for force generation are uncertain. We now report high-resolution structures showing new transitions in the kinesin mechanochemical cycle, including power stroke fluctuations upon ATP binding and a post-hydrolysis state with bound ADP + free phosphate. We find that rate-limiting ADP release occurs upon microtubule binding, accompanied by central β-sheet twisting, which triggers the power stroke - stalk rotation and neck mimic docking - upon ATP binding. Microtubule release occurs with β-strand-to-loop transitions, implying that β-strand refolding induces Pi release and the recovery stroke. The strained β-sheet during the power stroke and strand-to-loop transitions identify the β-sheet as the long-sought motor spring.
History
DepositionApr 3, 2024-
Header (metadata) releaseOct 8, 2025-
Map releaseOct 8, 2025-
UpdateOct 8, 2025-
Current statusOct 8, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39669.png

Downloads & links

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Map

FileDownload / File: emd_39669.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.75 Å/pix.
x 600 pix.
= 451.2 Å		0.75 Å/pix.
x 600 pix.
= 451.2 Å		0.75 Å/pix.
x 600 pix.
= 451.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.752 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.001
Minimum - Maximum-0.0029384461 - 0.011587556
Average (Standard dev.)0.00024439907 (±0.00137)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 451.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_39669_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_39669_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Kinesin-microtubule complex

EntireName: Kinesin-microtubule complex
Components
  • Complex: Kinesin-microtubule complex
    • Complex: Tubulin
      • Protein or peptide: Tubulin alpha-1B chain Q2XVP4
      • Protein or peptide: Tubulin beta-5B chain Q767L7
    • Complex: NCD
      • Protein or peptide: NCD

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Supramolecule #1: Kinesin-microtubule complex

SupramoleculeName: Kinesin-microtubule complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 200 kDa/nm

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Supramolecule #2: Tubulin

SupramoleculeName: Tubulin / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Sus scrofa (pig)

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Supramolecule #3: NCD

SupramoleculeName: NCD / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Drosophila melanogaster (fruit fly)

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Macromolecule #1: Tubulin alpha-1B chain Q2XVP4

MacromoleculeName: Tubulin alpha-1B chain Q2XVP4 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
SequenceString: MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVD LEPTVIDEVR TGTYRQLFHP EQLITGKEDA ANNYARGHYT IGKEIIDLVL D RIRKLADQ CTGLQGFLVF HSFGGGTGSG FTSLLMERLS VDYGKKSKLE ...String:
MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVD LEPTVIDEVR TGTYRQLFHP EQLITGKEDA ANNYARGHYT IGKEIIDLVL D RIRKLADQ CTGLQGFLVF HSFGGGTGSG FTSLLMERLS VDYGKKSKLE FSIYPAPQVS TA VVEPYNS ILTTHTTLEH SDCAFMVDNE AIYDICRRNL DIERPTYTNL NRLISQIVSS ITA SLRFDG ALNVDLTEFQ TNLVPYPRIH FPLATYAPVI SAEKAYHEQL SVAEITNACF EPAN QMVKC DPRHGKYMAC CLLYRGDVVP KDVNAAIATI KTKRSIQFVD WCPTGFKVGI NYQPP TVVP GGDLAKVQRA VCMLSNTTAI AEAWARLDHK FDLMYAKRAF VHWYVGEGME EGEFSE ARE DMAALEKDYE EVGVDSVEGE GEEEGEEY

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Macromolecule #2: Tubulin beta-5B chain Q767L7

MacromoleculeName: Tubulin beta-5B chain Q767L7 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
SequenceString: MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGTYHGDS DLQLDRISVY YNEATGGKYV PRAILVDLE PGTMDSVRSG PFGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV V RKEAESCD CLQGFQLTHS LGGGTGSGMG TLLISKIREE YPDRIMNTFS ...String:
MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGTYHGDS DLQLDRISVY YNEATGGKYV PRAILVDLE PGTMDSVRSG PFGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV V RKEAESCD CLQGFQLTHS LGGGTGSGMG TLLISKIREE YPDRIMNTFS VVPSPKVSDT VV EPYNATL SVHQLVENTD ETYCIDNEAL YDICFRTLKL TTPTYGDLNH LVSATMSGVT TCL RFPGQL NADLRKLAVN MVPFPRLHFF MPGFAPLTSR GSQQYRALTV PELTQQVFDA KNMM AACDP RHGRYLTVAA VFRGRMSMKE VDEQMLNVQN KNSSYFVEWI PNNVKTAVCD IPPRG LKMA VTFIGNSTAI QELFKRISEQ FTAMFRRKAF LHWYTGEGMD EMEFTEAESN MNDLVS EYQ QYQDATAEEE EDFGEEAEEE A

UniProtKB: Tubulin beta chain

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Macromolecule #3: NCD

MacromoleculeName: NCD / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster
Recombinant expressionOrganism: Escherichia coli
SequenceString: MESRLPKPSG LKKPQMPIKT VLPTDRIRAG LGGGAAGAGA FNVNANQTYC GNLLPPLSRD LNNLPQVLER RGGGARAASP EPMKLGHRAK LRRSRSACDI NELRGNKRTA AAPSLPSIPS KVSRLGGALT VSSQRLVRPA APSSITATAV KRPPVTRPAP RAAGGAAAKK ...String:
MESRLPKPSG LKKPQMPIKT VLPTDRIRAG LGGGAAGAGA FNVNANQTYC GNLLPPLSRD LNNLPQVLER RGGGARAASP EPMKLGHRAK LRRSRSACDI NELRGNKRTA AAPSLPSIPS KVSRLGGALT VSSQRLVRPA APSSITATAV KRPPVTRPAP RAAGGAAAKK PAGTGAAASS GAAAAAPKRI APYDFKARFH DLLEKHKVLK TKYEKQTEDM GELESMPQQL EETQNKLIET ESSLKNTQSD NECLQRQVKQ HTAKIETITS TLGRTKEELS ELQAIHEKVK TEHAALSTEV VHLRQRTEEL LRCNEQQAAE LETCKEQLFQ SNMERKELHN TVMDLRGNIR VFCRIRPPLE SEENRMCCTW TYHDESTVEL QSIDAQAKSK MGQQIFSFDQ VFHPLSSQSD IFEMVSPLIQ SALDGYNICI FAYGQTGSGK TYTMDGVPES VGVIPRTVDL LFDSIRGYRN LGWEYEIKAT FLEIYNEVLY DLLSNEQKDM EIRMAKNNKN DIYVSNITEE TVLDPNHLRH LMHTAKMNRA TASTAGNERS SRSHAVTKLE LIGRHAEKQE ISVGSINLVD LAGSESPKTS TRMTETKNIN RSLSELTNVI LALLQKQDHI PYRNSKLTHL LMPSLGGNSK TLMFINVSPF QDCFQESVKS LRFAASVNSC KMTKAKRNRY LNNSVANSST QSNNSGSFDK

UniProtKB: Protein claret segregational

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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: 6.8
Component:
ConcentrationFormulaName
100.0 mMPIPESPIPES
1.0 mMMgCl2MgCl2
1.0 mMEGTAEGTA
1.0 mMGTPGTP
1.0 mMAMPPNPAMPPNP

Details: 100 mM PIPES pH 6.8, 1 mM MgCl2, 1 mM EGTA, 1 mM GTP and 1 mM AMPPNP
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 310 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.8 µm

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 8.69668 Å
Applied symmetry - Helical parameters - Δ&Phi: -25.7385 °
Applied symmetry - Helical parameters - Axial symmetry: C14 (14 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 30431
CTF correctionSoftware - Name: RELION (ver. 3.1.4) / Type: NONE
Startup modelType of model: NONE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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