9DXE | pdb_00009dxe

Model of tubulin dimers used for determining the dimer rise in a taxol-stabilized microtubule

• PDB DOI: https://doi.org/10.2210/pdb9DXE/pdb
• EM Map EMD-47285: EMDB EMDataResource

• Classification: STRUCTURAL PROTEIN
• Organism(s): Sus scrofa
• Mutation(s): No 


• Deposited: 2024-10-11 Released: 2025-07-16 
• Deposition Author(s): Perez-Bertoldi, J.M., Nogales, E.
• Funding Organization(s): European Research Council (ERC), Howard Hughes Medical Institute (HHMI), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: HELICAL ARRAY 
• Reconstruction Method: HELICAL 

Literature

HURP regulates Kif18A recruitment and activity to synergistically control microtubule dynamics.

Perez-Bertoldi, J.M., Zhao, Y., Thawani, A., Yildiz, A., Nogales, E.

(2024) Nat Commun 15: 9687-9687

• PubMed: 39516196 
• DOI: https://doi.org/10.1038/s41467-024-53691-7
• Primary Citation of Related Structures:  
  9DHZ, 9DI0, 9DXC, 9DXE


• PubMed Abstract: 
  

  During mitosis, microtubule dynamics are regulated to ensure proper alignment and segregation of chromosomes. The dynamics of kinetochore-attached microtubules are regulated by hepatoma-upregulated protein (HURP) and the mitotic kinesin-8 Kif18A, but the underlying mechanism remains elusive. Using single-molecule imaging in vitro, we demonstrate that Kif18A motility is regulated by HURP. While sparse decoration of HURP activates the motor, higher concentrations hinder processive motility. To shed light on this behavior, we determine the binding mode of HURP to microtubules using cryo-EM. The structure helps rationalize why HURP functions as a microtubule stabilizer. Additionally, HURP partially overlaps with the microtubule-binding site of the Kif18A motor domain, indicating that excess HURP inhibits Kif18A motility by steric exclusion. We also observe that HURP and Kif18A function together to suppress dynamics of the microtubule plus-end, providing a mechanistic basis for how they collectively serve in microtubule length control.

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Organizational Affiliation: 
• Biophysics Graduate Group, University of California, Berkeley, CA, USA.
Physics Department, University of California, Berkeley, CA, USA.
Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
Biophysics Graduate Group, University of California, Berkeley, CA, USA. [e-mail].
Physics Department, University of California, Berkeley, CA, USA. [e-mail].
Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA. [e-mail].
Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. [e-mail].
Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA. [e-mail].
Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. [e-mail].
Howard Hughes Medical Institute, University of California, Berkeley, CA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 202.21 kDa 
• Atom Count: 13,502 
• Modeled Residue Count: 1,708 
• Deposited Residue Count: 1,792 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin alpha-1B chain	A, C	451	Sus scrofa	Mutation(s): 0  EC: 3.6.5
UniProt
Find proteins for Q2XVP4 (Sus scrofa) Explore Q2XVP4  Go to UniProtKB:  Q2XVP4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin beta chain	B, D	445	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for P02554 (Sus scrofa) Explore P02554  Go to UniProtKB:  P02554

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GTP	E [auth A], H [auth C]	GUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O14 P3 XKMLYUALXHKNFT-UUOKFMHZSA-N
GDP	G [auth B], J [auth D]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG	F [auth A], I [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: HELICAL ARRAY 
• Reconstruction Method: HELICAL 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-16 
Deposition Author(s): Perez-Bertoldi, J.M., Nogales, E.

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Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	--
Howard Hughes Medical Institute (HHMI)	United States	--
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History  

• Version 1.0: 2025-07-16
  Type: Initial release