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- EMDB-39664: Kinesin-14 in nucleotide-free state bound to 13 PF Microtubule -

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Basic information

Entry
Database: EMDB / ID: EMD-39664
TitleKinesin-14 in nucleotide-free state bound to 13 PF Microtubule
Map data
Sample
  • Complex: Kinesin-microtubule complex
    • Complex: Tubulin
      • Protein or peptide: Tubulin alpha-1B chain
      • Protein or peptide: Tubulin beta chain
    • Complex: NCD
      • Protein or peptide: Protein claret segregational
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
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 / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Resolution of Sister Chromatid Cohesion / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Mitotic Prometaphase / Carboxyterminal post-translational modifications of tubulin / RHOH GTPase cycle / EML4 and NUDC in mitotic spindle formation / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / PKR-mediated signaling / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / Aggrephagy / mitotic centrosome separation / meiotic spindle / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / Recruitment of NuMA to mitotic centrosomes / minus-end-directed microtubule motor activity / spindle organization / COPI-mediated anterograde transport / 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 / microtubule cytoskeleton / cell body / microtubule binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / 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 / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. ...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 / 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
Protein claret segregational / Tubulin alpha-1B chain / Tubulin beta chain
Similarity search - Component
Biological speciesSus scrofa (pig) / Drosophila melanogaster (fruit fly)
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_39664.png

Downloads & links

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Map

FileDownload / File: emd_39664.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)

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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-0.018479826 - 0.03455546
Average (Standard dev.)0.00026511986 (±0.002247097)
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_39664_half_map_1.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_39664_half_map_2.map
Projections & Slices
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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
      • Protein or peptide: Tubulin beta chain
    • Complex: NCD
      • Protein or peptide: Protein claret segregational
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Kinesin-microtubule complex

SupramoleculeName: Kinesin-microtubule complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
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

MacromoleculeName: Tubulin alpha-1B chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 50.204445 KDa
SequenceString: MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVDL EPTVIDEVRT GTYRQLFHP EQLITGKEDA ANNYARGHYT IGKEIIDLVL DRIRKLADQC TGLQGFLVFH SFGGGTGSGF TSLLMERLSV D YGKKSKLE ...String:
MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVDL EPTVIDEVRT GTYRQLFHP EQLITGKEDA ANNYARGHYT IGKEIIDLVL DRIRKLADQC TGLQGFLVFH SFGGGTGSGF TSLLMERLSV D YGKKSKLE FSIYPAPQVS TAVVEPYNSI LTTHTTLEHS DCAFMVDNEA IYDICRRNLD IERPTYTNLN RLISQIVSSI TA SLRFDGA LNVDLTEFQT NLVPYPRIHF PLATYAPVIS AEKAYHEQLS VAEITNACFE PANQMVKCDP RHGKYMACCL LYR GDVVPK DVNAAIATIK TKRSIQFVDW CPTGFKVGIN YQPPTVVPGG DLAKVQRAVC MLSNTTAIAE AWARLDHKFD LMYA KRAFV HWYVGEGMEE GEFSEAREDM AALEKDYEEV GVDSVEGEGE EEGEEY

UniProtKB: Tubulin alpha-1B chain

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Macromolecule #2: Tubulin beta chain

MacromoleculeName: Tubulin beta chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 49.717629 KDa
SequenceString: MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGTYHGDS DLQLDRISVY YNEATGGKYV PRAILVDLEP GTMDSVRSGP FGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV VRKEAESCDC LQGFQLTHSL GGGTGSGMGT LLISKIREEY P DRIMNTFS ...String:
MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGTYHGDS DLQLDRISVY YNEATGGKYV PRAILVDLEP GTMDSVRSGP FGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV VRKEAESCDC LQGFQLTHSL GGGTGSGMGT LLISKIREEY P DRIMNTFS VVPSPKVSDT VVEPYNATLS VHQLVENTDE TYCIDNEALY DICFRTLKLT TPTYGDLNHL VSATMSGVTT CL RFPGQLN ADLRKLAVNM VPFPRLHFFM PGFAPLTSRG SQQYRALTVP ELTQQVFDAK NMMAACDPRH GRYLTVAAVF RGR MSMKEV DEQMLNVQNK NSSYFVEWIP NNVKTAVCDI PPRGLKMAVT FIGNSTAIQE LFKRISEQFT AMFRRKAFLH WYTG EGMDE MEFTEAESNM NDLVSEYQQY QDATAEEEED FGEEAEEEA

UniProtKB: Tubulin beta chain

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Macromolecule #3: Protein claret segregational

MacromoleculeName: Protein claret segregational / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 46.450453 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MHAALSTEVV HLRQRTEELL RCNEQQAAEL ETCKEQLFQS NMERKELHNT VMDLRGNIRV FCRIRPPLES EENRMCCTWT YHDESTVEL QSIDAQAKSK MGQQIFSFDQ VFHPLSSQSD IFEMVSPLIQ SALDGYNICI FAYGQTGSGK TYTMDGVPES V GVIPRTVD ...String:
MHAALSTEVV HLRQRTEELL RCNEQQAAEL ETCKEQLFQS NMERKELHNT VMDLRGNIRV FCRIRPPLES EENRMCCTWT YHDESTVEL QSIDAQAKSK MGQQIFSFDQ VFHPLSSQSD IFEMVSPLIQ SALDGYNICI FAYGQTGSGK TYTMDGVPES V GVIPRTVD LLFDSIRGYR NLGWEYEIKA TFLEIKNEVL YDLLSNEQKD MEIRMAKNNK NDIYVSNITE ETVLDPNHLR HL MHTAKMN RATASTAGNE RSSRSHAVTK LELIGRHAEK QEISVGSINL VDLAGSESPK TSTRMTETKN INRSLSELTN VIL ALLQKQ DHIPYRNSKL THLLMPSLGG NSKTLMFINV SPFQDCFQES VKSLRFAASV NSCKMTKAKR NRYLNNSVAN SSTQ SNNSG NFDK

UniProtKB: Protein claret segregational

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Macromolecule #4: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 1 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

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

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Macromolecule #5: GUANOSINE-5'-DIPHOSPHATE

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

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

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Macromolecule #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #7: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 7 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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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

Details: 100 mM PIPES pH 6.8, 1 mM MgCl2, 1 mM EGTA, and 1 mM GTP
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: 9.40476 Å
Applied symmetry - Helical parameters - Δ&Phi: -27.6921 °
Applied symmetry - Helical parameters - Axial symmetry: C13 (13 fold cyclic)
Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 20390
CTF correctionSoftware - Name: RELION (ver. 3.1.4) / Type: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1cz7


Details: lowpass filtered
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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