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- PDB-9dmi: Structure of the C-terminal half of LRRK2 bound to RN277 (Type-II... -

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Basic information

Entry
Database: PDB / ID: 9dmi
TitleStructure of the C-terminal half of LRRK2 bound to RN277 (Type-II inhibitor)
Components
  • E11 DARPin
  • Leucine-rich repeat serine/threonine-protein kinase 2
KeywordsPROTEIN BINDING / GTPase / Kinase / inhibitors
Function / homology
Function and homology information


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 / regulation of cell projection organization / tangential migration from the subventricular zone to the olfactory bulb / GTP-dependent protein kinase activity ...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 / regulation of cell projection organization / tangential migration from the subventricular zone to the olfactory bulb / GTP-dependent protein kinase activity / regulation of SNARE complex assembly / regulation of neuroblast proliferation / regulation of ER to Golgi vesicle-mediated transport / protein localization to endoplasmic reticulum exit site / peroxidase inhibitor activity / negative regulation of late endosome to lysosome transport / regulation of mitochondrial depolarization / : / positive regulation of dopamine receptor signaling pathway / amphisome / regulation of synaptic vesicle transport / : / regulation of CAMKK-AMPK signaling cascade / co-receptor binding / negative regulation of GTPase activity / regulation of dopamine receptor signaling pathway / positive regulation of microglial cell activation / regulation of neuron maturation / regulation of retrograde transport, endosome to Golgi / cytoplasmic side of mitochondrial outer membrane / cellular response to curcumin / negative regulation of autophagosome assembly / olfactory bulb development / positive regulation of synaptic vesicle endocytosis / JUN kinase kinase kinase activity / multivesicular body, internal vesicle / negative regulation of excitatory postsynaptic potential / regulation of cAMP/PKA signal transduction / striatum development / neuron projection arborization / mitochondrion localization / regulation of dendritic spine morphogenesis / protein localization to mitochondrion / cellular response to dopamine / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / endoplasmic reticulum organization / positive regulation of protein autoubiquitination / negative regulation of protein processing / Wnt signalosome / positive regulation of programmed cell death / GTP metabolic process / regulation of canonical Wnt signaling pathway / syntaxin-1 binding / regulation of reactive oxygen species metabolic process / PTK6 promotes HIF1A stabilization / Golgi-associated vesicle / lysosome organization / clathrin binding / negative regulation of macroautophagy / regulation of mitochondrial fission / regulation of synaptic vesicle exocytosis / Lewy body / regulation of locomotion / intracellular distribution of mitochondria / Golgi organization / neuromuscular junction development / protein kinase A binding / microvillus / autolysosome / exploration behavior / locomotory exploration behavior / endoplasmic reticulum exit site / negative regulation of Notch signaling pathway / MAP kinase kinase kinase activity / regulation of synaptic vesicle endocytosis / canonical Wnt signaling pathway / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / Rho protein signal transduction / regulation of synaptic transmission, glutamatergic / presynaptic cytosol / phagocytic vesicle / JNK cascade / cellular response to manganese ion / neuron projection morphogenesis / positive regulation of autophagy / dendrite cytoplasm / positive regulation of protein ubiquitination / cellular response to starvation / GTPase activator activity / regulation of autophagy / determination of adult lifespan / SNARE binding / cellular response to reactive oxygen species / trans-Golgi network / mitochondrion organization / calcium-mediated signaling / regulation of protein stability / tubulin binding / regulation of membrane potential / excitatory postsynaptic potential
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 / Rab subfamily of small GTPases / Leucine-rich repeat domain superfamily / 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
: / Leucine-rich repeat serine/threonine-protein kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.35 Å
AuthorsSanz-Murillo, M. / Leschziner, A.
Funding support United States, 1items
OrganizationGrant numberCountry
Michael J. Fox FoundationASAP-000519 United States
CitationJournal: Sci Adv / Year: 2025
Title: Type II kinase inhibitors that target Parkinson's disease-associated LRRK2.
Authors: Nicolai D Raig / Katherine J Surridge / Marta Sanz-Murillo / Verena Dederer / Andreas Krämer / Martin P Schwalm / Nicholas M Lattal / Lewis Elson / Deep Chatterjee / Sebastian Mathea / ...Authors: Nicolai D Raig / Katherine J Surridge / Marta Sanz-Murillo / Verena Dederer / Andreas Krämer / Martin P Schwalm / Nicholas M Lattal / Lewis Elson / Deep Chatterjee / Sebastian Mathea / Thomas Hanke / Andres E Leschziner / Samara L Reck-Peterson / Stefan Knapp /
Abstract: Increased kinase activity of leucine-rich repeat kinase 2 (LRRK2) is associated with Parkinson's disease (PD). Numerous LRRK2-selective type I kinase inhibitors have been developed, and some have ...Increased kinase activity of leucine-rich repeat kinase 2 (LRRK2) is associated with Parkinson's disease (PD). Numerous LRRK2-selective type I kinase inhibitors have been developed, and some have entered clinical trials. Here, to our knowledge, we present the first type II kinase inhibitors that target LRRK2. Targeting the inactive conformation of LRRK2 is functionally distinct from targeting the active-like conformation using type I inhibitors. We designed these inhibitors with a combinatorial chemistry approach fusing selective LRRK2 type I and promiscuous type II inhibitors using iterative cycles of synthesis supported by structural biology and activity testing. Our lead compounds are selective and potent toward both LRRK2 and LRRK1, a close relative of LRRK2. Through cellular assays, cryo-electron microscopy structural analysis, and in vitro motility assays, we show that our inhibitors stabilize the open, inactive LRRK2 kinase conformation. These new conformation-specific compounds will be invaluable as tools to study LRRK2's function and regulation and expand the potential therapeutic options for PD.
History
DepositionSep 13, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Leucine-rich repeat serine/threonine-protein kinase 2
B: E11 DARPin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,5273
Polymers155,9422
Non-polymers5851
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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


Mass: 136174.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LRRK2, PARK8 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q5S007, non-specific serine/threonine protein kinase, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
#2: Protein E11 DARPin


Mass: 19766.912 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Some loops are missing due to the lack of cryo-EM density
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-A1A7Q / N-[3-tert-butyl-1-(4-methylphenyl)-1H-pyrazol-5-yl]-N'-{(3M)-3-[2-chloro-4-(morpholin-4-yl)-7H-pyrrolo[2,3-d]pyrimidin-5-yl]phenyl}urea


Mass: 585.099 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H33ClN8O2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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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: C-terminal half of LRRK2 bound to RN277 / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.137 MDa / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPES1
2150 mMSodium ChlorideNaCl1
32.5 mMMagnesium ChlorideMgCl21
45 %GlycerolGlyOH1
520 uMGDP1
60.5 mMTCEP1
SpecimenConc.: 616.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: UltrAuFoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277.15 K / Details: Blot time 4s Blot force 5 Waiting time 20s

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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 magnification: 130000 X / Nominal defocus max: 4000 nm / Nominal defocus min: 1000 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 55 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 13972

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Processing

EM software
IDNameVersionCategory
1Topaz0.2.5particle selection
2cryoSPARC4.5image acquisition
4cryoSPARC4.3CTF correction
7UCSF ChimeraX1.7model fitting
12cryoSPARC4.43D reconstruction
13PHENIX1.21model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.35 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 226172 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Atomic model buildingPDB-ID: 6VP7

6vp7


Pdb chain-ID: A / Accession code: 6VP7 / Chain residue range: 1333-2527 / Pdb chain residue range: 1333-2527 / Source name: PDB / Type: experimental model
RefinementHighest resolution: 3.35 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0068105
ELECTRON MICROSCOPYf_angle_d0.89711026
ELECTRON MICROSCOPYf_dihedral_angle_d6.071104
ELECTRON MICROSCOPYf_chiral_restr0.0541316
ELECTRON MICROSCOPYf_plane_restr0.0071376

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