4J7B

Crystal structure of polo-like kinase 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis for the inhibition of Polo-like kinase 1

Xu, J.Shen, C.Wang, T.Quan, J.

(2013) Nat Struct Mol Biol 20: 1047-1053

  • DOI: https://doi.org/10.1038/nsmb.2623
  • Primary Citation of Related Structures:  
    4J7B

  • PubMed Abstract: 

    Polo-like kinase 1 (PLK1) is a master regulator of mitosis and is considered a potential drug target for cancer therapy. PLK1 is characterized by an N-terminal kinase domain (KD) and a C-terminal Polo-box domain (PBD). The KD and PBD are mutually inhibited, but the molecular mechanisms of the autoinhibition remain unclear. Here we report the 2.3-Å crystal structure of the complex of the Danio rerio KD and PBD together with a PBD-binding motif of Drosophila melanogaster microtubule-associated protein 205 (Map205(PBM)). The structure reveals that the PBD binds and rigidifies the hinge region of the KD in a distinct conformation from that of the phosphopeptide-bound PBD. This structure provides a framework for understanding the autoinhibitory mechanisms of PLK1 and also sheds light on the activation mechanisms of PLK1 by phosphorylation or phosphopeptide binding.


  • Organizational Affiliation

    Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Polo-like kinase
A, D
297Danio rerioMutation(s): 2 
Gene Names: plk1
EC: 2.7.11.21
UniProt
Find proteins for Q6DRK7 (Danio rerio)
Explore Q6DRK7 
Go to UniProtKB:  Q6DRK7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6DRK7
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Polo-like kinase
B, E
237Danio rerioMutation(s): 1 
Gene Names: plk1
EC: 2.7.11.21
UniProt
Find proteins for Q6DRK7 (Danio rerio)
Explore Q6DRK7 
Go to UniProtKB:  Q6DRK7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6DRK7
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
205 kDa microtubule-associated protein
C, F
58Drosophila melanogasterMutation(s): 0 
Gene Names: Map205CG1483
UniProt
Find proteins for P23226 (Drosophila melanogaster)
Explore P23226 
Go to UniProtKB:  P23226
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23226
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.208 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.681α = 89.15
b = 57.453β = 89.84
c = 125.736γ = 72.38
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-07-24
    Type: Initial release
  • Version 1.1: 2013-09-18
    Changes: Database references
  • Version 1.2: 2016-06-08
    Changes: Derived calculations
  • Version 1.3: 2023-11-08
    Changes: Data collection, Database references, Refinement description