9FJH | pdb_00009fjh

Two PLK1 PBD proteins bound to CENP-U(58-114) phosphorylated at Thr78 and Thr98

• PDB DOI: https://doi.org/10.2210/pdb9FJH/pdb

• Classification: CELL CYCLE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-05-31 Released: 2025-09-24 
• Deposition Author(s): Ren, L., Gasper, R., Vetter, I.R., Musacchio, A.
• Funding Organization(s): European Research Council (ERC), German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.250 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.217 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Starting Model: experimental

Literature

Molecular anatomy of PLK1 master docking motifs.

Ren, L., Esposito-Verza, A., Gasper, R., Pesenti, M.E., Janning, P., Muller, F., Koerner, C., Geue, P., Wohlgemuth, S., Vetter, I.R., Musacchio, A.

(2026) Nat Commun 17

• PubMed: 42115593 
• DOI: https://doi.org/10.1038/s41467-026-73038-8
• Primary Citation Related Structures: 
  9FJG, 9FJH, 9FJI, 9FJJ


• PubMed Abstract: 
  

  The Polo-box domain (PBD) localizes Polo-like kinase 1 (PLK1) near mitotic substrates required for chromosome biorientation. Recent work on mitotic kinetochores showed PLK1 docking begins hierarchically at master docking motifs on BUB1 and CENP-U. Whether master docking motifs have common molecular features remains poorly understood. Presence on CENP-U of two neighbouring motifs generated by initial CDK1 priming and subsequent PLK1 phosphorylation led us to hypothesize PBD dimerization might be involved. Using biochemical, biophysical, and modelling approaches, we gathered strong evidence that CENP-U contains a single master docking motif. The motif is very high affinity and sufficient to form extensive interactions with the PBD, engaging multiple pockets on its surface without obvious added benefits from dimerization. Comparisons with motifs in BUB1, BUBR1, and PRC1 suggest commonalities of master PLK1 docking motifs. We discuss the implications of our observations for the mechanism of PLK1 activation.

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Organizational Affiliation: 
• Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany.
Crystallography and Biophysics Facility, Max Planck Institute of Molecular Physiology, Dortmund, Germany.
Mass Spectrometry Core Facility, Max Planck Institute of Molecular Physiology, Dortmund, Germany.
Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany. [e-mail].
Centre for Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 67.18 kDa 
• Atom Count: 4,069 
• Modeled Residue Count: 485 
• Deposited Residue Count: 581 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase PLK1	A, B	261	Homo sapiens	Mutation(s): 0  Gene Names: PLK1, PLK EC: 2.7.11.21
UniProt & NIH Common Fund Data Resources
Find proteins for P53350 (Homo sapiens) Explore P53350  Go to UniProtKB:  P53350
PHAROS:  P53350 GTEx:  ENSG00000166851

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Centromere protein U	C	59	Homo sapiens	Mutation(s): 0  Gene Names: CENPU, ICEN24, KLIP1, MLF1IP, PBIP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q71F23 (Homo sapiens) Explore Q71F23  Go to UniProtKB:  Q71F23
PHAROS:  Q71F23 GTEx:  ENSG00000151725

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	F [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE	D [auth A], E [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PO4 (Subject of Investigation/LOI)	G [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPO	C	L-PEPTIDE LINKING	C4 H10 N O6 P		THR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.250 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.217 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.89	α = 90
b = 135.09	β = 90
c = 60.95	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-09-24 
Deposition Author(s): Ren, L., Gasper, R., Vetter, I.R., Musacchio, A.

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Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	951430
German Research Foundation (DFG)	Germany	1430

Revision History  

• Version 1.0: 2025-09-24
  Type: Initial release
  
• Version 1.1: 2026-10-07
  Changes: Database references