9N9G | pdb_00009n9g

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

PDB DOI: https://doi.org/10.2210/pdb9N9G/pdb
EM Map EMD-49168: EMDB EMDataResource

Classification: CELL CYCLE
Organism(s): Homo sapiens, Sus scrofa
Expression System: Escherichia coli BL21(DE3)
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: 3.00 Å
Aggregation State: FILAMENT
Reconstruction Method: SINGLE PARTICLE

Starting Models: experimental, other, integrative
View more details

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: 535.95 kDa
Atom Count: 20,986
Modeled Residue Count: 2,617
Deposited Residue Count: 4,661
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kinetochore protein NDC80 homolog	A [auth 1], E [auth N], I [auth n]	645	Homo sapiens	Mutation(s): 0 Gene Names: NDC80, HEC, HEC1, KNTC2
UniProt & NIH Common Fund Data Resources
Find proteins for O14777 (Homo sapiens) Explore O14777 Go to UniProtKB: O14777
PHAROS: O14777 GTEx: ENSG00000080986
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O14777
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin alpha-1B chain	B [auth A], F [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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2XVP4
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin beta chain	C [auth B], G [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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02554
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Kinetochore protein Nuf2	D [auth F], H [auth f]	467	Homo sapiens	Mutation(s): 0 Gene Names: NUF2, CDCA1, NUF2R
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BZD4 (Homo sapiens) Explore Q9BZD4 Go to UniProtKB: Q9BZD4
PHAROS: Q9BZD4 GTEx: ENSG00000143228
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9BZD4
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 N [auth B] SDF format, chain S [auth b] MOL2 format, chain N [auth B] MOL2 format, chain S [auth b] mmCIF format, chain N [auth B] mmCIF format, chain S [auth b]	N [auth B], S [auth b]	TAXOL C₄₇ H₅₁ N O₁₄ RCINICONZNJXQF-MZXODVADSA-N		Interactions Focus chain N [auth B] Focus chain S [auth b] Interactions & Density Focus chain N [auth B] Focus chain S [auth b]
GTP Query on GTP Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain O [auth a] MOL2 format, chain J [auth A] MOL2 format, chain O [auth a] mmCIF format, chain J [auth A] mmCIF format, chain O [auth a]	J [auth A], O [auth a]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain J [auth A] Focus chain O [auth a] Interactions & Density Focus chain J [auth A] Focus chain O [auth a]
GDP Query on GDP Download Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain R [auth b] MOL2 format, chain L [auth B] MOL2 format, chain R [auth b] mmCIF format, chain L [auth B] mmCIF format, chain R [auth b]	L [auth B], R [auth b]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain L [auth B] Focus chain R [auth b] Interactions & Density Focus chain L [auth B] Focus chain R [auth b]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain M [auth B] SDF format, chain Q [auth a] SDF format, chain P [auth a] MOL2 format, chain K [auth A] MOL2 format, chain M [auth B] MOL2 format, chain Q [auth a] MOL2 format, chain P [auth a] mmCIF format, chain K [auth A] mmCIF format, chain M [auth B] mmCIF format, chain Q [auth a] mmCIF format, chain P [auth a]	K [auth A], M [auth B], P [auth a], Q [auth a]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain M [auth B] Focus chain P [auth a] Focus chain Q [auth a] Interactions & Density Focus chain K [auth A] Focus chain M [auth B] Focus chain P [auth a] Focus chain Q [auth a]