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- PDB-9yxq: Cryo-EM structure of the Xenopus laevis mitotic centromere-associ... -

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Basic information

Entry
Database: PDB / ID: 9yxq
TitleCryo-EM structure of the Xenopus laevis mitotic centromere-associated kinesin (MCAK) bound to the paclitaxel-stabilized microtubule
Components
  • Kinesin-like protein KIF2C
  • Tubulin alpha-1B chain
  • Tubulin beta chain
KeywordsCELL CYCLE / microtubule / MCAK / kinesin / mitosis
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
GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / TAXOL / Tubulin beta chain / Tubulin alpha-1B chain / Kinesin-like protein KIF2C
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
Sus scrofa (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.39 Å
AuthorsFunabiki, H. / Niu, Y.
Funding support United States, 1items
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, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Feb 4, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: Tubulin alpha-1B chain
2: Tubulin beta chain
3: Tubulin alpha-1B chain
4: Tubulin beta chain
5: Tubulin beta chain
6: Tubulin alpha-1B chain
7: Tubulin beta chain
8: Tubulin alpha-1B chain
A: Tubulin alpha-1B chain
B: Tubulin beta chain
M: Kinesin-like protein KIF2C
a: Tubulin alpha-1B chain
b: Tubulin beta chain
m: Kinesin-like protein KIF2C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)779,30643
Polymers768,11714
Non-polymers11,18929
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 3 types, 14 molecules 1368Aa2457BbMm

#1: Protein
Tubulin alpha-1B chain / Alpha-tubulin ubiquitous / Tubulin K-alpha-1 / Tubulin alpha-ubiquitous chain


Mass: 50204.445 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Brain / Plasmid details: https://www.cytoskeleton.com/t240 / References: UniProt: Q2XVP4
#2: Protein
Tubulin beta chain / Beta-tubulin


Mass: 49907.770 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: Brain / Plasmid details: https://www.cytoskeleton.com/t240 / References: UniProt: P02554
#3: Protein Kinesin-like protein KIF2C / Kinesin central motor 1 / xKCM1


Mass: 83721.766 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: kif2c, kcm1 / Cell line (production host): HEK293S GnTI- / Production host: Homo sapiens (human) / References: UniProt: Q91636

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Non-polymers , 4 types, 29 molecules

#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#6: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#7: Chemical
ChemComp-TA1 / TAXOL


Mass: 853.906 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C47H51NO14 / Comment: medication, chemotherapy*YM

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Details

Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: The Xenopus laevis mitotic centromere-associated kinesin (MCAK) bound to the paclitaxel-stabilized microtubule
Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightValue: 0.333 MDa / Experimental value: NO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293S GnTI-
Buffer solutionpH: 6.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 54.6 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategoryFitting-ID
1cryoSPARCparticle selection
7Cootmodel fitting1
9PHENIXmodel refinement1
10ISOLDEmodel refinement1
16cryoSPARC3D reconstruction
17RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.39 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 109829 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model building
IDProtocolSpaceTarget criteria
1AB INITIO MODELREALFSC=0.5
2
Atomic model building
IDPDB-IDPdb chain-ID 3D fitting-IDAccession codeChain-IDInitial refinement model-IDSource nameTypeChain residue rangeDetails
17SGS

7sgs

117SGS11PDBexperimental model
27SGS

7sgs

417SGS41PDBexperimental model
37SGS

7sgs

A17SGSA1PDBexperimental model
47SGS

7sgs

a17SGSa1PDBexperimental model
57SGS

7sgs

217SGS21PDBexperimental model
67SGS

7sgs

B17SGSB1PDBexperimental model
77SGS

7sgs

317SGS31PDBexperimental model
87SGS

7sgs

b17SGSb1PDBexperimental model
91MOtherother197-591Structure of MCAK class1 from this study was manually docked into density and refined by Coot and ISOLDE
102
112
122
132
142
152
162
172
182
192

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