Crystal structure of LRRK2 WD40 domain dimer

Experimental Data Snapshot

  • Resolution: 2.70 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.237 

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Crystal structure of the WD40 domain dimer of LRRK2.

Zhang, P.Fan, Y.Ru, H.Wang, L.Magupalli, V.G.Taylor, S.S.Alessi, D.R.Wu, H.

(2019) Proc Natl Acad Sci U S A 116: 1579-1584

  • DOI: https://doi.org/10.1073/pnas.1817889116
  • Primary Citation of Related Structures:  
    6DLO, 6DLP

  • PubMed Abstract: 

    Leucine-rich repeat kinase 2 (LRRK2) is a large multidomain protein with both a Ras of complex (ROC) domain and a kinase domain (KD) and, therefore, exhibits both GTPase and kinase activities. Human genetics studies have linked LRRK2 as a major genetic contributor to familial and sporadic Parkinson's disease (PD), a neurodegenerative movement disorder that inflicts millions worldwide. The C-terminal region of LRRK2 is a Trp-Asp-40 (WD40) domain with poorly defined biological functions but has been implicated in microtubule interaction. Here, we present the crystal structure of the WD40 domain of human LRRK2 at 2.6-Å resolution, which reveals a seven-bladed WD40 fold. The structure displays a dimeric assembly in the crystal, which we further confirm by measurements in solution. We find that structure-based and PD-associated disease mutations in the WD40 domain including the common G2385R polymorphism mainly compromise dimer formation. Assessment of full-length LRRK2 kinase activity by measuring phosphorylation of Rab10, a member of the family of Rab GTPases known to be important kinase substrates of LRRK2, shows enhancement of kinase activity by several dimerization-defective mutants including G2385R, although dimerization impairment does not always result in kinase activation. Furthermore, mapping of phylogenetically conserved residues onto the WD40 domain structure reveals surface patches that may be important for additional functions of LRRK2. Collectively, our analyses provide insights for understanding the structures and functions of LRRK2 and suggest the potential utility of LRRK2 kinase inhibitors in treating PD patients with WD40 domain mutations.

  • Organizational Affiliation

    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Leucine-rich repeat serine/threonine-protein kinase 2A [auth B],
B [auth A]
389Homo sapiensMutation(s): 0 
Gene Names: LRRK2PARK8
UniProt & NIH Common Fund Data Resources
Find proteins for Q5S007 (Homo sapiens)
Explore Q5S007 
Go to UniProtKB:  Q5S007
GTEx:  ENSG00000188906 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5S007
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.70 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.237 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.293α = 90
b = 103.59β = 90
c = 112.664γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-09
    Type: Initial release
  • Version 1.1: 2019-01-23
    Changes: Data collection, Database references
  • Version 1.2: 2019-02-13
    Changes: Data collection, Database references
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references