9YQK | pdb_00009yqk

C-terminal LRRK2 bound to C12 DARPin

• PDB DOI: https://doi.org/10.2210/pdb9YQK/pdb
• EM Map EMD-73338: EMDB EMDataResource

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Spodoptera frugiperda, Escherichia coli
• Mutation(s): No 


• Deposited: 2025-10-15 Released: 2026-08-12 
• Deposition Author(s): Sanz-Murillo, M., Leschziner, A.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

The structural basis for LRRK2's activation and autoinhibition.

Villagran Suarez, A., Hatch, K.S., Bodrug, T., Gai, W., Surridge, K.J., Moussikhina, E., Nguyen, K.H.V., Sanz-Murillo, M., Callahan, R., Xiong, E., Ramos, D., Zhu, L., Dederer, V., Mathea, S., Iwasa, J., Knapp, S., Shokat, K.M., Reck-Peterson, S.L., Leschziner, A.E.

(2026) Cell 

• PubMed: 42575089 
• DOI: https://doi.org/10.1016/j.cell.2026.07.027
• Primary Citation Related Structures: 
  9OM2, 9OXH, 9OXI, 9OYA, 9Y67, 9Y68, 9YQK


• PubMed Abstract: 
  

  Mutations in leucine-rich repeat kinase 2 (LRRK2) are the second most common cause of autosomal-dominant Parkinson's disease (PD), and increased LRRK2 kinase activity is also observed in idiopathic PD, making LRRK2 a major actionable therapeutic target. LRRK2 is a 286-kDa multidomain enzyme containing a Ras-like GTPase (ROC) and a kinase domain. Using cryo-electron microscopy (cryo-EM), biochemical reconstitution, and cell-based assays, we show that the ROC GTPase governs switching between autoinhibited and active states: GTP binding promotes activation, whereas GDP binding enforces autoinhibition. Two common PD-linked mutations, G2019S and R1441C/G/H, activate LRRK2 through distinct structural mechanisms, revealing genotype-specific routes to dysregulation. These findings provide a unified framework for understanding LRRK2 regulation with broad therapeutic implications. Stabilizing the guanosine diphosphate (GDP)-bound state may inhibit LRRK2 by maintaining autoinhibition, whereas promoting the GTP-bound state could be advantageous in specific cellular contexts, such as the lung, where increased LRRK2 kinase activity may play protective or regulatory roles.

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Organizational Affiliation: 
• Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94143, USA.
Institute of Pharmaceutical Chemistry and Structural Genomics Consortium, Goethe-University Frankfurt am Main, Frankfurt, Germany.
Department of Biochemistry, University of Utah, Salt Lake City, UT 84132, USA.
Institute of Pharmaceutical Chemistry and Structural Genomics Consortium, Goethe-University Frankfurt am Main, Frankfurt, Germany; LRRK2 Investigative Therapeutics Exchange (LITE), New York, NY 10120, USA.
Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94143, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; LRRK2 Investigative Therapeutics Exchange (LITE), New York, NY 10120, USA.
Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Department of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093, USA; LRRK2 Investigative Therapeutics Exchange (LITE), New York, NY 10120, USA. Electronic address: [e-mail].
Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA; LRRK2 Investigative Therapeutics Exchange (LITE), New York, NY 10120, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 300.81 kDa 
• Atom Count: 8,925 
• Modeled Residue Count: 1,123 
• Deposited Residue Count: 2,658 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Leucine-rich repeat serine/threonine-protein kinase 2	A	2,527	Homo sapiens	Mutation(s): 0  Gene Names: LRRK2 EC: 2.7.11.1 (UniProt), 3.6.5 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q5S007 (Homo sapiens) Explore Q5S007  Go to UniProtKB:  Q5S007
GTEx:  ENSG00000188906

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
C12 DARPin	B	131	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.1
MODEL REFINEMENT	PHENIX	1.21_5207

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-08-12 
Deposition Author(s): Sanz-Murillo, M., Leschziner, A.

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Funding Organization	Location	Grant Number
Other private	United States	ASAP-000519

Revision History  

• Version 1.0: 2026-08-12
  Type: Initial release
  
• Version 1.1: 2026-08-19
  Changes: Data collection, Database references