8FO9 | pdb_00008fo9

Cryo-EM structure of Rab29-LRRK2 complex in the LRRK2 tetramer state

PDB DOI: https://doi.org/10.2210/pdb8FO9/pdb
EM Map EMD-29342: EMDB EMDataResource

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Homo sapiens, Escherichia coli
Mutation(s): No

Deposited: 2022-12-30 Released: 2024-01-03
Deposition Author(s): Zhu, H., Sun, J.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.48 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

PubMed: 38127736 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1126/science.adi9926
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 1,189.99 kDa
Atom Count: 53,742
Modeled Residue Count: 7,253
Deposited Residue Count: 10,462
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Leucine-rich repeat serine/threonine-protein kinase 2	A, B [auth C], E, F	2,527	Homo sapiens	Mutation(s): 0 Gene Names: LRRK2, PARK8 EC: 2.7.11.1 (PDB Primary Data), 3.6.5 (PDB Primary Data)
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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5S007
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ras-related protein Rab-7L1	C [auth B], D	177	Homo sapiens	Mutation(s): 0 Gene Names: RAB29, RAB7L1 EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for O14966 (Homo sapiens) Explore O14966 Go to UniProtKB: O14966
PHAROS: O14966 GTEx: ENSG00000117280
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O14966
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP (Subject of Investigation/LOI) Query on ATP Download:Ideal Coordinates CCD File SDF format, chain N [auth F] SDF format, chain L [auth E] SDF format, chain J [auth C] SDF format, chain H [auth A] MOL2 format, chain N [auth F] MOL2 format, chain L [auth E] MOL2 format, chain J [auth C] MOL2 format, chain H [auth A] mmCIF format, chain N [auth F] mmCIF format, chain L [auth E] mmCIF format, chain J [auth C] mmCIF format, chain H [auth A]	H [auth A], J [auth C], L [auth E], N [auth F]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain H [auth A] Focus chain J [auth C] Focus chain L [auth E] Focus chain N [auth F] Interactions & Density Focus chain H [auth A] Focus chain J [auth C] Focus chain L [auth E] Focus chain N [auth F]
GDP (Subject of Investigation/LOI) Query on GDP Download:Ideal Coordinates CCD File SDF format, chain M [auth F] SDF format, chain K [auth E] SDF format, chain I [auth C] SDF format, chain G [auth A] MOL2 format, chain M [auth F] MOL2 format, chain K [auth E] MOL2 format, chain I [auth C] MOL2 format, chain G [auth A] mmCIF format, chain M [auth F] mmCIF format, chain K [auth E] mmCIF format, chain I [auth C] mmCIF format, chain G [auth A]	G [auth A], I [auth C], K [auth E], M [auth F]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain G [auth A] Focus chain I [auth C] Focus chain K [auth E] Focus chain M [auth F] Interactions & Density Focus chain G [auth A] Focus chain I [auth C] Focus chain K [auth E] Focus chain M [auth F]