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- PDB-9ybl: LRRK2 asymmetric dimer -

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Basic information

Entry
Database: PDB / ID: 9ybl
TitleLRRK2 asymmetric dimer
ComponentsLeucine-rich repeat serine/threonine-protein kinase 2
KeywordsHYDROLASE / Kinase / Gtpases / LRRK2
Function / homology
Function and homology information


regulation of neuron maturation / caveola neck / : / beta-catenin destruction complex binding / regulation of branching morphogenesis of a nerve / Wnt signalosome assembly / negative regulation of motile cilium assembly / regulation of kidney size / tangential migration from the subventricular zone to the olfactory bulb / regulation of cell projection organization ...regulation of neuron maturation / caveola neck / : / beta-catenin destruction complex binding / regulation of branching morphogenesis of a nerve / Wnt signalosome assembly / negative regulation of motile cilium assembly / regulation of kidney size / tangential migration from the subventricular zone to the olfactory bulb / regulation of cell projection organization / regulation of dopamine receptor signaling pathway / regulation of ER to Golgi vesicle-mediated transport / GTP-dependent protein kinase activity / regulation of SNARE complex assembly / regulation of neuroblast proliferation / protein localization to endoplasmic reticulum exit site / negative regulation of late endosome to lysosome transport / regulation of mitochondrial depolarization / : / peroxidase inhibitor activity / positive regulation of dopamine receptor signaling pathway / amphisome / regulation of synaptic vesicle transport / : / regulation of CAMKK-AMPK signaling cascade / striatum development / negative regulation of autophagosome assembly / co-receptor binding / positive regulation of microglial cell activation / olfactory bulb development / regulation of retrograde transport, endosome to Golgi / negative regulation of GTPase activity / cellular response to curcumin / regulation of locomotion / positive regulation of synaptic vesicle endocytosis / JUN kinase kinase kinase activity / cytoplasmic side of mitochondrial outer membrane / endoplasmic reticulum organization / regulation of cAMP/PKA signal transduction / negative regulation of excitatory postsynaptic potential / multivesicular body, internal vesicle / neuron projection arborization / regulation of dendritic spine morphogenesis / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / mitochondrion localization / protein localization to mitochondrion / cellular response to dopamine / negative regulation of protein processing / Wnt signalosome / positive regulation of protein autoubiquitination / exploration behavior / GTP metabolic process / regulation of reactive oxygen species metabolic process / regulation of canonical Wnt signaling pathway / lysosome organization / syntaxin-1 binding / positive regulation of programmed cell death / negative regulation of macroautophagy / PTK6 promotes HIF1A stabilization / Golgi-associated vesicle / clathrin binding / regulation of synaptic vesicle exocytosis / locomotory exploration behavior / Golgi organization / regulation of mitochondrial fission / intracellular distribution of mitochondria / Lewy body / protein kinase A binding / canonical Wnt signaling pathway / microvillus / neuromuscular junction development / autolysosome / endoplasmic reticulum exit site / Rho protein signal transduction / determination of adult lifespan / MAP kinase kinase kinase activity / JNK cascade / regulation of synaptic vesicle endocytosis / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / regulation of synaptic transmission, glutamatergic / presynaptic cytosol / cellular response to manganese ion / phagocytic vesicle / neuron projection morphogenesis / positive regulation of autophagy / dendrite cytoplasm / excitatory postsynaptic potential / positive regulation of protein ubiquitination / cellular response to starvation / GTPase activator activity / calcium-mediated signaling / mitochondrion organization / SNARE binding / negative regulation of neuron projection development / cellular response to reactive oxygen species / trans-Golgi network / regulation of protein stability / regulation of membrane potential / tubulin binding / regulation of autophagy
Similarity search - Function
: / : / : / LRRK2 ARM repeat / LRRK2 ANK repeat / LRRK2 beta propeller / : / : / C-terminal of Roc, COR-B domain / C-terminal of Roc (COR) domain ...: / : / : / LRRK2 ARM repeat / LRRK2 ANK repeat / LRRK2 beta propeller / : / : / C-terminal of Roc, COR-B domain / C-terminal of Roc (COR) domain / C-terminal of Roc, COR-A domain / Ras of Complex, Roc, domain of DAPkinase / Roc domain profile. / Roc domain / Leucine-rich repeats, bacterial type / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Rab subfamily of small GTPases / Ankyrin repeat-containing domain superfamily / Armadillo-like helical / Small GTP-binding protein domain / Armadillo-type fold / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Leucine-rich repeat serine/threonine-protein kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.44 Å
AuthorsVillagran Suarez, A. / Bodrug, T. / Leschziner, A.
Funding support United States, 1items
OrganizationGrant numberCountry
Aligning Science Across Parkinsons (ASAP) United States
CitationJournal: Cell(Cambridge,Mass.) / Year: 2026
Title: The structural basis for LRRK2's activation and autoinhibition
Authors: 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. ...Authors: 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.
History
DepositionSep 17, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 19, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Leucine-rich repeat serine/threonine-protein kinase 2
A: Leucine-rich repeat serine/threonine-protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)573,3693
Polymers572,9262
Non-polymers4431
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Leucine-rich repeat serine/threonine-protein kinase 2


Mass: 286462.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LRRK2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q5S007
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Leucine Rich Repeat Kinase 2 asymmetric dimer / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 55 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20.1_4487model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.44 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 79889 / Symmetry type: POINT
RefinementHighest resolution: 3.44 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00415804
ELECTRON MICROSCOPYf_angle_d0.88621470
ELECTRON MICROSCOPYf_dihedral_angle_d5.8942180
ELECTRON MICROSCOPYf_chiral_restr0.0522546
ELECTRON MICROSCOPYf_plane_restr0.0082728

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