9YXQ | pdb_00009yxq

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

PDB DOI: https://doi.org/10.2210/pdb9YXQ/pdb
EM Map EMD-73614: EMDB EMDataResource

Classification: CELL CYCLE
Organism(s): Sus scrofa, Xenopus laevis
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2025-10-27 Released: 2026-02-04
Deposition Author(s): Funabiki, H., Niu, Y.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.39 Å
Aggregation State: FILAMENT
Reconstruction Method: SINGLE PARTICLE

Starting Models: experimental, other
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Cryo-EM structure of the human Hec1-Nuf2 dimer bound to the paclitaxel-stabilized microtubule

Funabiki, H., Niu, Y.

(2026) Sci Adv

Macromolecule Content

Total Structure Weight: 779.31 kDa
Atom Count: 47,551
Modeled Residue Count: 5,950
Deposited Residue Count: 6,854
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin alpha-1B chain	A [auth 1] C [auth 3] F [auth 6] H [auth 8] I [auth A] A [auth 1], C [auth 3], F [auth 6], H [auth 8], I [auth A], L [auth a]	451	Sus scrofa	Mutation(s): 0 EC: 3.6.5
UniProt
Find proteins for Q2XVP4 (Sus scrofa) Explore Q2XVP4 Go to UniProtKB: Q2XVP4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q2XVP4
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin beta chain	B [auth 2] D [auth 4] E [auth 5] G [auth 7] J [auth B] B [auth 2], D [auth 4], E [auth 5], G [auth 7], J [auth B], M [auth b]	445	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for P02554 (Sus scrofa) Explore P02554 Go to UniProtKB: P02554
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02554
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Kinesin-like protein KIF2C	K [auth M], N [auth m]	739	Xenopus laevis	Mutation(s): 0 Gene Names: kif2c, kcm1
UniProt
Find proteins for Q91636 (Xenopus laevis) Explore Q91636 Go to UniProtKB: Q91636
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q91636
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TA1 Query on TA1 Download:Ideal Coordinates CCD File SDF format, chain EA [auth 7] SDF format, chain LA [auth B] SDF format, chain PA [auth b] SDF format, chain R [auth 2] SDF format, chain Z [auth 5] SDF format, chain W [auth 4] MOL2 format, chain EA [auth 7] MOL2 format, chain LA [auth B] MOL2 format, chain PA [auth b] MOL2 format, chain R [auth 2] MOL2 format, chain Z [auth 5] MOL2 format, chain W [auth 4] mmCIF format, chain EA [auth 7] mmCIF format, chain LA [auth B] mmCIF format, chain PA [auth b] mmCIF format, chain R [auth 2] mmCIF format, chain Z [auth 5] mmCIF format, chain W [auth 4]	EA [auth 7] LA [auth B] PA [auth b] R [auth 2] W [auth 4] EA [auth 7], LA [auth B], PA [auth b], R [auth 2], W [auth 4], Z [auth 5]	TAXOL C₄₇ H₅₁ N O₁₄ RCINICONZNJXQF-MZXODVADSA-N		Interactions Focus chain EA [auth 7] Focus chain LA [auth B] Focus chain PA [auth b] Focus chain R [auth 2] Focus chain W [auth 4] Focus chain Z [auth 5] Interactions & Density Focus chain EA [auth 7] Focus chain LA [auth B] Focus chain PA [auth b] Focus chain R [auth 2] Focus chain W [auth 4] Focus chain Z [auth 5]
GTP Query on GTP Download:Ideal Coordinates CCD File SDF format, chain AA [auth 6] SDF format, chain FA [auth 8] SDF format, chain P [auth 1] SDF format, chain S [auth 3] SDF format, chain MA [auth a] SDF format, chain HA [auth A] MOL2 format, chain AA [auth 6] MOL2 format, chain FA [auth 8] MOL2 format, chain P [auth 1] MOL2 format, chain S [auth 3] MOL2 format, chain MA [auth a] MOL2 format, chain HA [auth A] mmCIF format, chain AA [auth 6] mmCIF format, chain FA [auth 8] mmCIF format, chain P [auth 1] mmCIF format, chain S [auth 3] mmCIF format, chain MA [auth a] mmCIF format, chain HA [auth A]	AA [auth 6] FA [auth 8] HA [auth A] MA [auth a] P [auth 1] AA [auth 6], FA [auth 8], HA [auth A], MA [auth a], P [auth 1], S [auth 3]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain AA [auth 6] Focus chain FA [auth 8] Focus chain HA [auth A] Focus chain MA [auth a] Focus chain P [auth 1] Focus chain S [auth 3] Interactions & Density Focus chain AA [auth 6] Focus chain FA [auth 8] Focus chain HA [auth A] Focus chain MA [auth a] Focus chain P [auth 1] Focus chain S [auth 3]
GDP Query on GDP Download:Ideal Coordinates CCD File SDF format, chain CA [auth 7] SDF format, chain JA [auth B] SDF format, chain Q [auth 2] SDF format, chain QA [auth b] SDF format, chain X [auth 5] SDF format, chain U [auth 4] MOL2 format, chain CA [auth 7] MOL2 format, chain JA [auth B] MOL2 format, chain Q [auth 2] MOL2 format, chain QA [auth b] MOL2 format, chain X [auth 5] MOL2 format, chain U [auth 4] mmCIF format, chain CA [auth 7] mmCIF format, chain JA [auth B] mmCIF format, chain Q [auth 2] mmCIF format, chain QA [auth b] mmCIF format, chain X [auth 5] mmCIF format, chain U [auth 4]	CA [auth 7] JA [auth B] Q [auth 2] QA [auth b] U [auth 4] CA [auth 7], JA [auth B], Q [auth 2], QA [auth b], U [auth 4], X [auth 5]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain CA [auth 7] Focus chain JA [auth B] Focus chain Q [auth 2] Focus chain QA [auth b] Focus chain U [auth 4] Focus chain X [auth 5] Interactions & Density Focus chain CA [auth 7] Focus chain JA [auth B] Focus chain Q [auth 2] Focus chain QA [auth b] Focus chain U [auth 4] Focus chain X [auth 5]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain BA [auth 6] SDF format, chain DA [auth 7] SDF format, chain GA [auth 8] SDF format, chain IA [auth A] SDF format, chain KA [auth B] SDF format, chain T [auth 3] SDF format, chain V [auth 4] SDF format, chain Y [auth 5] SDF format, chain OA [auth a] SDF format, chain O [auth 1] SDF format, chain NA [auth a] MOL2 format, chain BA [auth 6] MOL2 format, chain DA [auth 7] MOL2 format, chain GA [auth 8] MOL2 format, chain IA [auth A] MOL2 format, chain KA [auth B] MOL2 format, chain T [auth 3] MOL2 format, chain V [auth 4] MOL2 format, chain Y [auth 5] MOL2 format, chain OA [auth a] MOL2 format, chain O [auth 1] MOL2 format, chain NA [auth a] mmCIF format, chain BA [auth 6] mmCIF format, chain DA [auth 7] mmCIF format, chain GA [auth 8] mmCIF format, chain IA [auth A] mmCIF format, chain KA [auth B] mmCIF format, chain T [auth 3] mmCIF format, chain V [auth 4] mmCIF format, chain Y [auth 5] mmCIF format, chain OA [auth a] mmCIF format, chain O [auth 1] mmCIF format, chain NA [auth a]	BA [auth 6] DA [auth 7] GA [auth 8] IA [auth A] KA [auth B] BA [auth 6], DA [auth 7], GA [auth 8], IA [auth A], KA [auth B], NA [auth a], O [auth 1], OA [auth a], T [auth 3], V [auth 4], Y [auth 5]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BA [auth 6] Focus chain DA [auth 7] Focus chain GA [auth 8] Focus chain IA [auth A] Focus chain KA [auth B] Focus chain NA [auth a] Focus chain O [auth 1] Focus chain OA [auth a] Focus chain T [auth 3] Focus chain V [auth 4] Focus chain Y [auth 5] Interactions & Density Focus chain BA [auth 6] Focus chain DA [auth 7] Focus chain GA [auth 8] Focus chain IA [auth A] Focus chain KA [auth B] Focus chain NA [auth a] Focus chain O [auth 1] Focus chain OA [auth a] Focus chain T [auth 3] Focus chain V [auth 4] Focus chain Y [auth 5]