9N9I | pdb_00009n9i

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/pdb9N9I/pdb
EM Map EMD-49170: EMDB EMDataResource

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

Deposited: 2025-02-10 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: 3.30 Å
Aggregation State: FILAMENT
Reconstruction Method: SINGLE PARTICLE

Starting Models: experimental, other, integrative
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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: 491.65 kDa
Atom Count: 30,614
Modeled Residue Count: 3,831
Deposited Residue Count: 4,323
Unique protein chains: 3

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin alpha-1B chain	A [auth 1], C [auth 4], D [auth A], H [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 3], E [auth B], F [auth C], I [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	G [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 X [auth C] SDF format, chain V [auth B] SDF format, chain N [auth 3] SDF format, chain CA [auth b] MOL2 format, chain X [auth C] MOL2 format, chain V [auth B] MOL2 format, chain N [auth 3] MOL2 format, chain CA [auth b] mmCIF format, chain X [auth C] mmCIF format, chain V [auth B] mmCIF format, chain N [auth 3] mmCIF format, chain CA [auth b]	CA [auth b], N [auth 3], V [auth B], X [auth C]	TAXOL C₄₇ H₅₁ N O₁₄ RCINICONZNJXQF-MZXODVADSA-N		Interactions Focus chain CA [auth b] Focus chain N [auth 3] Focus chain V [auth B] Focus chain X [auth C] Interactions & Density Focus chain CA [auth b] Focus chain N [auth 3] Focus chain V [auth B] Focus chain X [auth C]
GTP Query on GTP Download:Ideal Coordinates CCD File SDF format, chain Y [auth a] SDF format, chain R [auth A] SDF format, chain P [auth 4] SDF format, chain J [auth 1] MOL2 format, chain Y [auth a] MOL2 format, chain R [auth A] MOL2 format, chain P [auth 4] MOL2 format, chain J [auth 1] mmCIF format, chain Y [auth a] mmCIF format, chain R [auth A] mmCIF format, chain P [auth 4] mmCIF format, chain J [auth 1]	J [auth 1], P [auth 4], R [auth A], Y [auth a]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain J [auth 1] Focus chain P [auth 4] Focus chain R [auth A] Focus chain Y [auth a] Interactions & Density Focus chain J [auth 1] Focus chain P [auth 4] Focus chain R [auth A] Focus chain Y [auth a]
GDP Query on GDP Download:Ideal Coordinates CCD File SDF format, chain W [auth C] SDF format, chain T [auth B] SDF format, chain L [auth 3] SDF format, chain AA [auth b] MOL2 format, chain W [auth C] MOL2 format, chain T [auth B] MOL2 format, chain L [auth 3] MOL2 format, chain AA [auth b] mmCIF format, chain W [auth C] mmCIF format, chain T [auth B] mmCIF format, chain L [auth 3] mmCIF format, chain AA [auth b]	AA [auth b], L [auth 3], T [auth B], W [auth C]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain AA [auth b] Focus chain L [auth 3] Focus chain T [auth B] Focus chain W [auth C] Interactions & Density Focus chain AA [auth b] Focus chain L [auth 3] Focus chain T [auth B] Focus chain W [auth C]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain Z [auth a] SDF format, chain U [auth B] SDF format, chain S [auth A] SDF format, chain Q [auth 4] SDF format, chain O [auth 4] SDF format, chain M [auth 3] SDF format, chain K [auth 1] SDF format, chain BA [auth b] MOL2 format, chain Z [auth a] MOL2 format, chain U [auth B] MOL2 format, chain S [auth A] MOL2 format, chain Q [auth 4] MOL2 format, chain O [auth 4] MOL2 format, chain M [auth 3] MOL2 format, chain K [auth 1] MOL2 format, chain BA [auth b] mmCIF format, chain Z [auth a] mmCIF format, chain U [auth B] mmCIF format, chain S [auth A] mmCIF format, chain Q [auth 4] mmCIF format, chain O [auth 4] mmCIF format, chain M [auth 3] mmCIF format, chain K [auth 1] mmCIF format, chain BA [auth b]	BA [auth b] K [auth 1] M [auth 3] O [auth 4] Q [auth 4] BA [auth b], K [auth 1], M [auth 3], O [auth 4], Q [auth 4], S [auth A], U [auth B], Z [auth a]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BA [auth b] Focus chain K [auth 1] Focus chain M [auth 3] Focus chain O [auth 4] Focus chain Q [auth 4] Focus chain S [auth A] Focus chain U [auth B] Focus chain Z [auth a] Interactions & Density Focus chain BA [auth b] Focus chain K [auth 1] Focus chain M [auth 3] Focus chain O [auth 4] Focus chain Q [auth 4] Focus chain S [auth A] Focus chain U [auth B] Focus chain Z [auth a]