3ZDU | pdb_00003zdu

Crystal structure of the human CDKL3 kinase domain

• PDB DOI: https://doi.org/10.2210/pdb3ZDU/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2012-11-30 Released: 2013-03-20 
• Deposition Author(s): Canning, P., Elkins, J.M., Goubin, S., Mahajan, P., Pike, A.C.W., Quigley, A., MacKenzie, A., Carpenter, E.P., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Bullock, A.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.262 (Depositor), 0.269 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.223 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Starting Models: experimental

Literature

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

• PubMed: 29420175 
• DOI: https://doi.org/10.1016/j.celrep.2017.12.083
• Primary Citation 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: 
• Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7DQ, UK.
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.
Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.
Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7DQ, UK. Electronic address: [e-mail].
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. 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)

Macromolecule Content 

• Total Structure Weight: 37.99 kDa 
• Atom Count: 2,516 
• Modeled Residue Count: 297 
• Deposited Residue Count: 325 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CYCLIN-DEPENDENT KINASE-LIKE 3	A	325	Homo sapiens	Mutation(s): 2  EC: 2.7.11.22
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IVW4 (Homo sapiens) Explore Q8IVW4  Go to UniProtKB:  Q8IVW4
PHAROS:  Q8IVW4 GTEx:  ENSG00000006837

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
38R	B [auth A]	[4-({4-[(3-cyclopentyl-1H-pyrazol-5-yl)amino]pyrimidin-2-yl}amino)phenyl]acetonitrile C20 H21 N7 VKAOLAKWGBXOCQ-UHFFFAOYSA-N
ZN	C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	F [auth A], G [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA	E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.262 (Depositor), 0.269 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.223 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.93	α = 90
b = 63.93	β = 90
c = 163.63	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-03-20 
Deposition Author(s): Canning, P., Elkins, J.M., Goubin, S., Mahajan, P., Pike, A.C.W., Quigley, A., MacKenzie, A., Carpenter, E.P., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Bullock, A.

Revision History  

• Version 1.0: 2013-03-20
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Database references, Structure summary
• Version 1.2: 2022-03-30
  Changes: Database references, Derived calculations, Other
• Version 1.3: 2023-12-20
  Changes: Data collection, Refinement description