8SMC

Cryo-EM structure of LRRK2 bound with type-I inhibitor DNL201

  • Classification: HYDROLASE
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): No 

  • Deposited: 2023-04-26 Released: 2024-01-03 
  • Deposition Author(s): Sun, J., Zhu, H.
  • Funding Organization(s): National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.02 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Rab29-dependent asymmetrical activation of leucine-rich repeat kinase 2.

Zhu, H.Tonelli, F.Turk, M.Prescott, A.Alessi, D.R.Sun, J.

(2023) Science 382: 1404-1411

  • DOI: https://doi.org/10.1126/science.adi9926
  • Primary Citation of Related Structures:  
    8FO2, 8FO8, 8FO9, 8SMC

  • PubMed Abstract: 

    Gain-of-function mutations in LRRK2 , which encodes the leucine-rich repeat kinase 2 (LRRK2), are the most common genetic cause of late-onset Parkinson's disease. LRRK2 is recruited to membrane organelles and activated by Rab29, a Rab guanosine triphosphatase encoded in the PARK16 locus. We present cryo-electron microscopy structures of Rab29-LRRK2 complexes in three oligomeric states, providing key snapshots during LRRK2 recruitment and activation. Rab29 induces an unexpected tetrameric assembly of LRRK2, formed by two kinase-active central protomers and two kinase-inactive peripheral protomers. The central protomers resemble the active-like state trapped by the type I kinase inhibitor DNL201, a compound that underwent a phase 1 clinical trial. Our work reveals the structural mechanism of LRRK2 spatial regulation and provides insights into LRRK2 inhibitor design for Parkinson's disease treatment.


  • Organizational Affiliation

    Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
non-specific serine/threonine protein kinaseA [auth C]1,201Homo sapiensMutation(s): 0 
Gene Names: LRRK2
UniProt & NIH Common Fund Data Resources
Find proteins for Q5S007 (Homo sapiens)
Explore Q5S007 
Go to UniProtKB:  Q5S007
PHAROS:  Q5S007
GTEx:  ENSG00000188906 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5S007
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GDP (Subject of Investigation/LOI)
Query on GDP

Download Ideal Coordinates CCD File 
B [auth C]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
TVT (Subject of Investigation/LOI)
Query on TVT

Download Ideal Coordinates CCD File 
C
2-methyl-2-(3-methyl-4-{[4-(methylamino)-5-(trifluoromethyl)pyrimidin-2-yl]amino}-1H-pyrazol-1-yl)propanenitrile
C14 H16 F3 N7
ZPPUMAMZIMPJGP-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.02 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesR00HL143037

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-03
    Type: Initial release