4J7B | pdb_00004j7b

Crystal structure of polo-like kinase 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.264 (Depositor), 0.261 (DCC) 
  • R-Value Work: 
    0.205 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 
    0.208 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 4J7B

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 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.

Macromolecule Content 

  • Total Structure Weight: 136 kDa 
  • Atom Count: 9,170 
  • Modeled Residue Count: 1,089 
  • Deposited Residue Count: 1,184 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  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
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
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
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
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
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.264 (Depositor), 0.261 (DCC) 
  • R-Value Work:  0.205 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 0.208 (Depositor) 
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