9F6S | pdb_00009f6s

PDZ domain in complex with the peptide from AP2-associated protein kinase 1

• PDB DOI: https://doi.org/10.2210/pdb9F6S/pdb

• Classification: CYTOSOLIC PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-05-02 Released: 2025-05-14 
• Deposition Author(s): Benova, V., Boura, E.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free: 
  0.213 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.201 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: experimental

Literature

AAK1-mediated phosphorylation of PDLIM5 and Talin1 promotes focal adhesion disassembly to accelerate cell migration.

Krocianova, D., Dagg, A.D., Clayton, R.A., Potesil, D., Fedorova, V., Harmanec, A., Benova, V., Bosakova, V., Kaufman, J.G.G., Martinkova, P., Alblova, M., Kelly, B.T., Hanakova, K., Roudnicky, P., Spielman, S.J., Fric, J., Sroubek, F., Houser, J., Wrobel, A.G., Boura, E., Owen, D.J., Zdrahal, Z., Kadlecova, Z.

(2026) Nat Commun 

• PubMed: 42082516 
• DOI: https://doi.org/10.1038/s41467-026-72501-w
• Primary Citation Related Structures: 
  9F6S


• PubMed Abstract: 
  

  AAK1 and BMP2K are serine/threonine kinases traditionally known for phosphorylating AP2 during clathrin-mediated endocytosis (CME), but their broader roles remained incompletely defined. Here, using motif-guided in silico, biochemical, and phosphoproteomic screens, we identify PDLIM5 and Talin1 as direct AAK1/BMP2K substrates. Despite high kinase-domain similarity, only AAK1 promotes cell migration and potentiates focal adhesion (FA) turnover. Live-cell imaging shows that AAK1 recruitment to FAs peaks as disassembly begins. The conserved AAK1 C-terminal PDZ-binding motif mediates direct, low-affinity binding to PDLIM5, providing a plausible mechanism for localized substrate access. Dynamic analyses of phospho-mimetic and phospho-null mutants support a model in which AAK1-dependent phosphorylation promotes timely release of PDLIM5 and Talin1 during FA disassembly. These findings reveal a kinase-driven contribution to FA turnover distinct from protease- and phosphatase-based mechanisms and suggest that functional divergence between AAK1 and BMP2K may provide a strategy to modulate cell migration with reduced impact on CME.

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Organizational Affiliation: 
• Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic.
Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge, UK.
CEITEC, Masaryk University, Brno, Czech Republic.
Czech Academy of Sciences, Institute of Information Theory and Automation, Prague, Czech Republic.
Faculty of Mathematics and Physics, Charles University, Prague, Czech Republic.
Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic.
International Clinical Research Center, St. Anne's University Hospital in Brno, Brno, Czech Republic.
Centre of Molecular Structure, Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Vestec, Czech Republic.
Childhood Cancer Data Lab, Alex's Lemonade Stand Foundation, Bala Cynwyd, PA, USA.
Institute of Hematology and Blood Transfusion, Prague, Czech Republic.
Core Facility Biomolecular Interactions and Crystallization, Masaryk University, Brno, Czech Republic.
Department of Biochemistry, University of Oxford, Oxford, UK.
Structural Biology of Disease Processes Laboratory, The Francis Crick Institute, London, UK.
Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic. [e-mail].
Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge, UK. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 10.07 kDa 
• Atom Count: 806 
• Modeled Residue Count: 90 
• Deposited Residue Count: 96 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PDZ and LIM domain protein 5	A	90	Homo sapiens	Mutation(s): 0  Gene Names: PDLIM5, ENH, L9
UniProt & NIH Common Fund Data Resources
Find proteins for Q96HC4 (Homo sapiens) Explore Q96HC4  Go to UniProtKB:  Q96HC4
PHAROS:  Q96HC4 GTEx:  ENSG00000163110

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
AP2-associated protein kinase 1	B	6	Homo sapiens	Mutation(s): 0  Gene Names: AAK1, KIAA1048 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q2M2I8 (Homo sapiens) Explore Q2M2I8  Go to UniProtKB:  Q2M2I8
PHAROS:  Q2M2I8 GTEx:  ENSG00000115977

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free:  0.213 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.201 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.93	α = 90
b = 37.84	β = 90
c = 52.39	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-05-14 
Deposition Author(s): Benova, V., Boura, E.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-05-14
  Type: Initial release
  
• Version 1.1: 2026-05-27
  Changes: Database references