Crystal structure of the human CDKL2 kinase domain

Experimental Data Snapshot

  • Resolution: 1.53 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 

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CDKL Family Kinases Have Evolved Distinct Structural Features and Ciliary Function.

Canning, P.Park, K.Goncalves, J.Li, C.Howard, C.J.Sharpe, T.D.Holt, L.J.Pelletier, L.Bullock, A.N.Leroux, M.R.

(2018) Cell Rep 22: 885-894

  • DOI: https://doi.org/10.1016/j.celrep.2017.12.083
  • Primary Citation of Related Structures:  
    3ZDU, 4AAA, 4AGU, 4BBM, 4BGQ

  • PubMed Abstract: 

    Various kinases, including a cyclin-dependent kinase (CDK) family member, regulate the growth and functions of primary cilia, which perform essential roles in signaling and development. Neurological disorders linked to CDK-Like (CDKL) proteins suggest that these underexplored kinases may have similar functions. Here, we present the crystal structures of human CDKL1, CDKL2, CDKL3, and CDKL5, revealing their evolutionary divergence from CDK and mitogen-activated protein kinases (MAPKs), including an unusual ?J helix important for CDKL2 and CDKL3 activity. C. elegans CDKL-1, most closely related to CDKL1-4 and localized to neuronal cilia transition zones, modulates cilium length; this depends on its kinase activity and ?J helix-containing C terminus. Human CDKL5, linked to Rett syndrome, also localizes to cilia, and it impairs ciliogenesis when overexpressed. CDKL5 patient mutations modeled in CDKL-1 cause localization and/or cilium length defects. Together, our studies establish a disease model system suggesting cilium length defects as a pathomechanism for neurological disorders, including epilepsy.

  • Organizational Affiliation

    Department of Molecular Biology and Biochemistry, and Centre for Cell Biology, Development, and Disease, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CYCLIN-DEPENDENT KINASE-LIKE 2331Homo sapiensMutation(s): 2 
Gene Names: CDKL2
UniProt & NIH Common Fund Data Resources
Find proteins for Q92772 (Homo sapiens)
Explore Q92772 
Go to UniProtKB:  Q92772
PHAROS:  Q92772
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92772
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.53 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.182 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.819α = 90
b = 70.22β = 90
c = 83.66γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2011-12-21
    Type: Initial release
  • Version 1.1: 2018-01-24
    Changes: Structure summary
  • Version 1.2: 2022-03-30
    Changes: Database references, Derived calculations, Other