9YGT | pdb_00009ygt

Leucine Rich Repeat Kinase 2 bound to GDP (from GMPPNP data)

PDB DOI: https://doi.org/10.2210/pdb9YGT/pdb
EM Map EMD-72941: EMDB EMDataResource

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

Deposited: 2025-09-29 Released: 2026-08-19
Deposition Author(s): Villagran, A., Bodrug, T.
Funding Organization(s): Michael J. Fox Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.42 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9YGT

This is version 1.0 of the entry. See complete history.

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., 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

DOI: https://doi.org/10.1016/j.cell.2026.07.027

Macromolecule Content

Total Structure Weight: 286.91 kDa
Atom Count: 13,934
Modeled Residue Count: 1,774
Deposited Residue Count: 2,527
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5S007
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GDP Query on GDP Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.42 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-08-19

Deposition Author(s):

Funding Organization	Location	Grant Number
Michael J. Fox Foundation	United States	ASAP-000519

Revision History (Full details and data files)

Version 1.0: 2026-08-19
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.