4NK7 | pdb_00004nk7

Crystal Structure of the D. melanogaster Plk4 cryptic polo box (CPB)

• PDB DOI: https://doi.org/10.2210/pdb4NK7/pdb

• Classification: TRANSFERASE
• Organism(s): Drosophila melanogaster
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-11-12 Released: 2014-08-27 
• Deposition Author(s): Dong, G., Lesigang, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.23 Å
• R-Value Free: 
  0.264 (Depositor), 0.268 (DCC) 
• R-Value Work: 
  0.240 (Depositor), 0.248 (DCC) 
• R-Value Observed: 
  0.243 (Depositor) 

Starting Model: experimental

Literature

Structure of the C. elegans ZYG-1 Cryptic Polo Box Suggests a Conserved Mechanism for Centriolar Docking of Plk4 Kinases.

Shimanovskaya, E., Viscardi, V., Lesigang, J., Lettman, M.M., Qiao, R., Svergun, D.I., Round, A., Oegema, K., Dong, G.

(2014) Structure 22: 1090-1104

• PubMed: 24980795 
• DOI: https://doi.org/10.1016/j.str.2014.05.009
• Primary Citation Related Structures: 
  4NK7, 4NKB


• PubMed Abstract: 
  

  Plk4 family kinases control centriole assembly. Plk4s target mother centrioles through an interaction between their cryptic polo box (CPB) and acidic regions in the centriolar receptors SPD-2/Cep192 and/or Asterless/Cep152. Here, we report a crystal structure for the CPB of C. elegans ZYG-1, which forms a Z-shaped dimer containing an intermolecular β sheet with an extended basic surface patch. Biochemical and in vivo analysis revealed that electrostatic interactions dock the ZYG-1 CPB basic patch onto the SPD-2-derived acidic region to promote ZYG-1 targeting and new centriole assembly. Analysis of a different crystal form of the Drosophila Plk4 (DmPlk4) CPB suggests that it also forms a Z-shaped dimer. Comparison of the ZYG-1 and DmPlk4 CPBs revealed structural changes in the ZYG-1 CPB that confer selectivity for binding SPD-2 over Asterless-derived acidic regions. Overall, our findings suggest a conserved mechanism for centriolar docking of Plk4 homologs that initiate daughter centriole assembly.

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Organizational Affiliation: 
• Max F. Perutz Laboratories, Medical University of Vienna, 1030 Vienna, Austria.
Department of Cellular and Molecular Medicine, Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA 92093, USA.
European Molecular Biology Laboratory, Hamburg Unit, EMBL c/o DESY, Notkestrasse 85, 22603 Hamburg, Germany.
European Molecular Biology Laboratory, Grenoble Outstation, 6 rue Jules Horowitz, 38042 Grenoble, France; Unit for Virus Host-Cell Interactions, University Grenoble Alpes-EMBL-CNRS, 6 rue Jules Horowitz, 38042 Grenoble, France.
Department of Cellular and Molecular Medicine, Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA 92093, USA. Electronic address: [e-mail].
Max F. Perutz Laboratories, Medical University of Vienna, 1030 Vienna, Austria. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 25.5 kDa 
• Atom Count: 1,705 
• Modeled Residue Count: 212 
• Deposited Residue Count: 223 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase PLK4	A	223	Drosophila melanogaster	Mutation(s): 0  Gene Names: CG7186, D. melanogaster Plk4 (residues 383-601), SAK EC: 2.7.11.21
UniProt
Find proteins for O97143 (Drosophila melanogaster) Explore O97143  Go to UniProtKB:  O97143

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.23 Å
• R-Value Free:  0.264 (Depositor), 0.268 (DCC) 
• R-Value Work:  0.240 (Depositor), 0.248 (DCC) 
• R-Value Observed: 0.243 (Depositor) 

Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 132.207	α = 90
b = 132.207	β = 90
c = 134.247	γ = 120

Software Package:

Software Name	Purpose
DNA	data collection
SOLVE	phasing
PHENIX	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-08-27 
Deposition Author(s): Dong, G., Lesigang, J.

Revision History  

• Version 1.0: 2014-08-27
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Refinement description