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- EMDB-73614: Cryo-EM structure of the Xenopus laevis mitotic centromere-associ... -

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Basic information

Entry
Database: EMDB / ID: EMD-73614
TitleCryo-EM structure of the Xenopus laevis mitotic centromere-associated kinesin (MCAK) bound to the paclitaxel-stabilized microtubule
Map data
Sample
  • Complex: The Xenopus laevis mitotic centromere-associated kinesin (MCAK) bound to the paclitaxel-stabilized microtubule
    • Protein or peptide: Tubulin alpha-1B chain
    • Protein or peptide: Tubulin beta chain
    • Protein or peptide: Kinesin-like protein KIF2C
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: TAXOL
Keywordsmicrotubule / MCAK / kinesin / mitosis / cell cycle
Function / homology
Function and homology information


metaphase chromosome alignment / microtubule plus-end / attachment of mitotic spindle microtubules to kinetochore / 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 ...metaphase chromosome alignment / microtubule plus-end / attachment of mitotic spindle microtubules to kinetochore / 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 / microtubule depolymerization / 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 / microtubule motor activity / Recruitment of NuMA to mitotic centrosomes / COPI-mediated anterograde transport / microtubule-based movement / kinetochore / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron migration / mitotic cell cycle / microtubule cytoskeleton / microtubule binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / cell division / GTPase activity / GTP binding / ATP binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
: / Kinesin-like protein KIF2A-like, N-terminal / 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 ...: / Kinesin-like protein KIF2A-like, N-terminal / 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
Tubulin beta chain / Tubulin alpha-1B chain / Kinesin-like protein KIF2C
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog) / Sus scrofa (pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.39 Å
AuthorsFunabiki H / Niu Y
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM132111 United States
CitationJournal: Sci Adv / Year: 2026
Title: Cryo-EM structure of the human Hec1-Nuf2 dimer bound to the paclitaxel-stabilized microtubule
Authors: Funabiki H / Niu Y
History
DepositionOct 27, 2025-
Header (metadata) releaseFeb 4, 2026-
Map releaseFeb 4, 2026-
UpdateFeb 4, 2026-
Current statusFeb 4, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73614.png

Downloads & links

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Map

FileDownload / File: emd_73614.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.16 Å/pix.
x 320 pix.
= 371.28 Å		1.16 Å/pix.
x 320 pix.
= 371.28 Å		1.16 Å/pix.
x 320 pix.
= 371.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.16025 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0017
Minimum - Maximum-0.0047760163 - 0.010446876
Average (Standard dev.)0.000015428539 (±0.000453324)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 371.27997 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_73614_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_73614_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_73614_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 : The Xenopus laevis mitotic centromere-associated kinesin (MCAK) b...

EntireName: The Xenopus laevis mitotic centromere-associated kinesin (MCAK) bound to the paclitaxel-stabilized microtubule
Components
  • Complex: The Xenopus laevis mitotic centromere-associated kinesin (MCAK) bound to the paclitaxel-stabilized microtubule
    • Protein or peptide: Tubulin alpha-1B chain
    • Protein or peptide: Tubulin beta chain
    • Protein or peptide: Kinesin-like protein KIF2C
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: TAXOL

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Supramolecule #1: The Xenopus laevis mitotic centromere-associated kinesin (MCAK) b...

SupramoleculeName: The Xenopus laevis mitotic centromere-associated kinesin (MCAK) bound to the paclitaxel-stabilized microtubule
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 333 KDa

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Macromolecule #1: Tubulin alpha-1B chain

MacromoleculeName: Tubulin alpha-1B chain / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig) / Organ: Brain
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: 6 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig) / Organ: Brain
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 FEEEGEEDEA

UniProtKB: Tubulin beta chain

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Macromolecule #3: Kinesin-like protein KIF2C

MacromoleculeName: Kinesin-like protein KIF2C / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 83.721766 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MERLVATRLV TGLAVKIMRS NGVIHNANIT SVNMDRSSVN VEWKEGEANK GKEISFADVI SVNPELLDAV LAPTNVKENM PPQRNVSSQ NHKRKTISKI PAPKEVAAKN SLLSESGAQS VLRERSTRMT AIHETLPYEN EMEAESTPLP IQQNSVQARS R STKVSIAE ...String:
MERLVATRLV TGLAVKIMRS NGVIHNANIT SVNMDRSSVN VEWKEGEANK GKEISFADVI SVNPELLDAV LAPTNVKENM PPQRNVSSQ NHKRKTISKI PAPKEVAAKN SLLSESGAQS VLRERSTRMT AIHETLPYEN EMEAESTPLP IQQNSVQARS R STKVSIAE EPRLQTRISE IVEESLPSGR NNQGRRKSNI VKEMEKMKNK REEQRAQNYE RRMKRAQDYD TSVPNWEFGK MI KEFRATM DCHRISMADP AEEHRICVCV RKRPLNKQEL SKKEIDIISV PSKNIVLVHE PKLKVDLTKY LENQAFRFDF SFD ETATNE VVYRFTARPL VQSIFEGGKA TCFAYGQTGS GKTHTMGGDF SGKSQNVSKG VYAFASRDVF LLLDQPRYKH LDLD VFVTF FEIYNGKVFD LLNKKTKLRV LEDAKQEVQV VGLLEKQVIS ADDVFKMIEI GSACRTSGQT FANTSSSRSH ACLQI ILRR GSKLHGKFSL VDLAGNERGV DTASADRITR MEGAEINRSL LALKECIRAL GQNKSHTPFR ESKLTQILRD SFIGEN SRT CMIAMLSPGF NSCEYTLNTL RYADRVKELS PQNAETNDDN LQMEDSGGSH ASIEGLQLQD DFLLKDEELS THNSFQD AL NRVGELEDKA VDELRELVQK EPEWTNLLQM TEQPDYDLEN FVMQAEYLIQ ERSKVLIALG DSINSLRLAL QVEEQASK Q ISKKKRSNKS NSLEVLFQ

UniProtKB: Kinesin-like protein KIF2C

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 11 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #5: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 6 / 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 #6: GUANOSINE-5'-DIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 6 / 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 #7: TAXOL

MacromoleculeName: TAXOL / type: ligand / ID: 7 / Number of copies: 6 / Formula: TA1
Molecular weightTheoretical: 853.906 Da
Chemical component information

ChemComp-TA1:
TAXOL / medication, chemotherapy*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 6.8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 54.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: AlphaFold
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 3.39 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: cryoSPARC, RELION) / Number images used: 109829
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChainDetails

7sgs

chain_id: 1, source_name: PDB, initial_model_type: experimental model

7sgs

chain_id: 4, source_name: PDB, initial_model_type: experimental model

7sgs

chain_id: A, source_name: PDB, initial_model_type: experimental model

7sgs

chain_id: a, source_name: PDB, initial_model_type: experimental model

7sgs

chain_id: 2, source_name: PDB, initial_model_type: experimental model

7sgs

chain_id: B, source_name: PDB, initial_model_type: experimental model

7sgs

chain_id: 3, source_name: PDB, initial_model_type: experimental model

7sgs

chain_id: b, source_name: PDB, initial_model_type: experimental model
chain_id: M, residue_range: 197-591, source_name: Other, initial_model_type: otherStructure of MCAK class1 from this study was manually docked into density and refined by Coot and ISOLDE
RefinementSpace: REAL / Protocol: AB INITIO MODEL / Target criteria: FSC=0.5
Output model

PDB-9yxq:
Cryo-EM structure of the Xenopus laevis mitotic centromere-associated kinesin (MCAK) bound to the paclitaxel-stabilized microtubule

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