8FAC | pdb_00008fac

Structure of the leucine-rich repeat kinase 1 monomer

• PDB DOI: https://doi.org/10.2210/pdb8FAC/pdb
• EM Map EMD-28950: EMDB EMDataResource

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2022-11-25 Released: 2023-08-16 
• Deposition Author(s): Metcalfe, R.D., Martinez Fiesco, J.A., Zhang, P.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.92 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure and regulation of full-length human leucine-rich repeat kinase 1.

Metcalfe, R.D., Martinez Fiesco, J.A., Bonet-Ponce, L., Kluss, J.H., Cookson, M.R., Zhang, P.

(2023) Nat Commun 14: 4797-4797

• PubMed: 37558661 
• DOI: https://doi.org/10.1038/s41467-023-40532-2
• Primary Citation Related Structures: 
  8FAC


• PubMed Abstract: 
  

  The human leucine-rich repeat kinases (LRRKs), LRRK1 and LRRK2 are large and unusually complex multi-domain kinases, which regulate fundamental cellular processes and have been implicated in human disease. Structures of LRRK2 have recently been determined, but the structure and molecular mechanisms regulating the activity of the LRRK1 as well as differences in the regulation of LRRK1 and LRRK2 remain unclear. Here, we report a cryo-EM structure of the LRRK1 monomer and a lower-resolution cryo-EM map of the LRRK1 dimer. The monomer structure, in which the kinase is in an inactive conformation, reveals key interdomain interfaces that control kinase activity as we validate experimentally. Both the LRRK1 monomer and dimer are structurally distinct compared to LRRK2. Overall, our results provide structural insights into the activation of the human LRRKs, which advance our understanding of their physiological and pathological roles.

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Organizational Affiliation: 
• Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA.
Cell Biology and Gene Expression Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, 20892, USA.
Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: light scattering

Macromolecule Content 

• Total Structure Weight: 230 kDa 
• Atom Count: 10,955 
• Modeled Residue Count: 1,377 
• Deposited Residue Count: 2,048 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Leucine-rich repeat serine/threonine-protein kinase 1	A	2,048	Homo sapiens	Mutation(s): 0  Gene Names: LRRK1, KIAA1790 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q38SD2 (Homo sapiens) Explore Q38SD2  Go to UniProtKB:  Q38SD2
PHAROS:  Q38SD2 GTEx:  ENSG00000154237

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	B [auth A]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.92 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-08-16 
Deposition Author(s): Metcalfe, R.D., Martinez Fiesco, J.A., Zhang, P.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	ZIA BC 011744

Revision History  

• Version 1.0: 2023-08-16
  Type: Initial release