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- EMDB-45609: Structure of the LRRK2/14-3-3 complex -

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Basic information

Entry
Database: EMDB / ID: EMD-45609
TitleStructure of the LRRK2/14-3-3 complex
Map data
Sample
  • Complex: Complex of LRRK2 monomer with 14-3-3 dimer
    • Complex: LRRK2
      • Protein or peptide: Leucine-rich repeat serine/threonine-protein kinase 2
    • Complex: 14-3-3 dimer
      • Protein or peptide: 14-3-3 protein gamma
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
KeywordsLRRK2 / LRRK2 complex / LRRK2 14-3-3 complex / LRRK2 autoinhibited / TRANSFERASE / TRANSFERASE-SIGNALING PROTEIN complex
Function / homology
Function and homology information


caveola neck / : / beta-catenin destruction complex binding / regulation of branching morphogenesis of a nerve / regulation of kidney size / Wnt signalosome assembly / 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 ...caveola neck / : / beta-catenin destruction complex binding / regulation of branching morphogenesis of a nerve / regulation of kidney size / Wnt signalosome assembly / 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 lysosomal lumen pH / positive regulation of cell-cell adhesion / regulation of CAMKK-AMPK signaling cascade / co-receptor binding / negative regulation of GTPase activity / phosphorylation-dependent protein binding / regulation of dopamine receptor signaling pathway / regulation of neuron maturation / positive regulation of microglial cell activation / regulation of retrograde transport, endosome to Golgi / positive regulation of synaptic vesicle endocytosis / negative regulation of excitatory postsynaptic potential / cytoplasmic side of mitochondrial outer membrane / negative regulation of autophagosome assembly / olfactory bulb development / JUN kinase kinase kinase activity / neuron projection arborization / striatum development / multivesicular body, internal vesicle / regulation of dendritic spine morphogenesis / positive regulation of T cell mediated immune response to tumor cell / mitochondrion localization / 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 / Wnt signalosome / negative regulation of protein processing / positive regulation of programmed cell death / regulation of canonical Wnt signaling pathway / GTP metabolic process / regulation of neuron differentiation / syntaxin-1 binding / regulation of reactive oxygen species metabolic process / lysosome organization / Golgi-associated vesicle / clathrin binding / PTK6 promotes HIF1A stabilization / negative regulation of macroautophagy / protein kinase C inhibitor activity / neuromuscular junction development / regulation of cAMP/PKA signal transduction / protein kinase A binding / regulation of mitochondrial fission / regulation of locomotion / regulation of synaptic vesicle exocytosis / microvillus / Golgi organization / intracellular distribution of mitochondria / exploration behavior / endoplasmic reticulum exit site / autolysosome / locomotory exploration behavior / Regulation of localization of FOXO transcription factors / negative regulation of Notch signaling pathway / Activation of BAD and translocation to mitochondria / regulation of signal transduction / MAP kinase kinase kinase activity / regulation of synaptic vesicle endocytosis / canonical Wnt signaling pathway / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / regulation of synaptic transmission, glutamatergic / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / protein targeting / negative regulation of protein kinase activity / cellular response to glucose starvation / presynaptic cytosol / Rho protein signal transduction / RHO GTPases activate PKNs / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / neuron projection morphogenesis / phagocytic vesicle / cellular response to manganese ion / JNK cascade / insulin-like growth factor receptor binding / negative regulation of TORC1 signaling / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome
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 / C-terminal of Roc, COR-A 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 / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein / 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 / WD40-repeat-containing domain superfamily / Serine/Threonine protein kinases, catalytic domain / 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
14-3-3 protein gamma / Leucine-rich repeat serine/threonine-protein kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.96 Å
AuthorsMartinez Fiesco JA / Zhang P
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Nat Commun / Year: 2025
Title: 14-3-3 binding maintains the Parkinson's associated kinase LRRK2 in an inactive state.
Authors: Juliana A Martinez Fiesco / Alexandra Beilina / Astrid Alvarez de la Cruz / Ning Li / Riley D Metcalfe / Mark R Cookson / Ping Zhang /
Abstract: Leucine-rich repeat kinase 2 (LRRK2) is an essential regulator in cellular signaling and a major contributor to Parkinson's disease (PD) pathogenesis. 14-3-3 proteins are critical modulators of LRRK2 ...Leucine-rich repeat kinase 2 (LRRK2) is an essential regulator in cellular signaling and a major contributor to Parkinson's disease (PD) pathogenesis. 14-3-3 proteins are critical modulators of LRRK2 activity, yet the structural basis of their interaction has remained unclear. Here, we present the cryo-electron microscopy structure of the LRRK2:14-3-3 autoinhibitory complex, revealing how a 14-3-3 dimer stabilizes an autoinhibited LRRK2 monomer through dual-site anchoring. The dimer engages both phosphorylated S910/S935 sites and the COR-A/B subdomains within the Roc-COR GTPase region. This spatial configuration constrains LRR domain mobility, reinforces the inactive conformation, and likely impedes LRRK2 dimerization and oligomer formation. Structure-guided mutagenesis studies show that PD-associated mutations at the COR:14-3-3 interface and within the GTPase domain weaken 14-3-3 binding and impair its inhibitory effect on LRRK2 kinase activity. Furthermore, we demonstrate that type I LRRK2 kinase inhibitor, which stabilizes the kinase domain in its active conformation, reduces 14-3-3 binding and promotes dephosphorylation at pS910 and pS935. Together, these findings provide a structural basis for understanding how LRRK2 is maintained in an inactive state, elucidate the mechanistic role of 14-3-3 in LRRK2 regulation, inform the interpretation of PD biomarkers, and suggest therapeutic strategies aimed at enhancing LRRK2-14-3-3 interactions to treat PD and related disorders.
History
DepositionJul 2, 2024-
Header (metadata) releaseSep 3, 2025-
Map releaseSep 3, 2025-
UpdateSep 3, 2025-
Current statusSep 3, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45609.png

Downloads & links

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Map

FileDownload / File: emd_45609.map.gz / Format: CCP4 / Size: 247.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.81 Å/pix.
x 402 pix.
= 325.62 Å		0.81 Å/pix.
x 402 pix.
= 325.62 Å		0.81 Å/pix.
x 402 pix.
= 325.62 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.81 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.122
Minimum - Maximum-0.0017893222 - 2.3597667
Average (Standard dev.)0.0008398179 (±0.019723173)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions402402402
Spacing402402402
CellA=B=C: 325.62 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_45609_additional_1.map
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Half map: #2

Fileemd_45609_half_map_1.map
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Half map: #1

Fileemd_45609_half_map_2.map
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Sample components

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Entire : Complex of LRRK2 monomer with 14-3-3 dimer

EntireName: Complex of LRRK2 monomer with 14-3-3 dimer
Components
  • Complex: Complex of LRRK2 monomer with 14-3-3 dimer
    • Complex: LRRK2
      • Protein or peptide: Leucine-rich repeat serine/threonine-protein kinase 2
    • Complex: 14-3-3 dimer
      • Protein or peptide: 14-3-3 protein gamma
  • Ligand: GUANOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Complex of LRRK2 monomer with 14-3-3 dimer

SupramoleculeName: Complex of LRRK2 monomer with 14-3-3 dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Molecular weightTheoretical: 342.7 kDa/nm

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Supramolecule #2: LRRK2

SupramoleculeName: LRRK2 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: 14-3-3 dimer

SupramoleculeName: 14-3-3 dimer / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: 14-3-3 protein gamma

MacromoleculeName: 14-3-3 protein gamma / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 30.436814 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSHHHHHHS GENLYFQGMV DREQLVQKAR LAEQAERYDD MAAAMKNVTE LNEPLSNEER NLLSVAYKNV VGARRSSWRV ISSIEQKTS ADGNEKKIEM VRAYREKIEK ELEAVCQDVL SLLDNYLIKN CSETQYESKV FYLKMKGDYY RYLAEVATGE K RATVVESS ...String:
MGSHHHHHHS GENLYFQGMV DREQLVQKAR LAEQAERYDD MAAAMKNVTE LNEPLSNEER NLLSVAYKNV VGARRSSWRV ISSIEQKTS ADGNEKKIEM VRAYREKIEK ELEAVCQDVL SLLDNYLIKN CSETQYESKV FYLKMKGDYY RYLAEVATGE K RATVVESS EKAYSEAHEI SKEHMQPTHP IRLGLALNYS VFYYEIQNAP EQACHLAKTA FDDAIAELDT LNEDSYKDST LI MQLLRDN LTLWTSDQQD DDGGEGNN

UniProtKB: 14-3-3 protein gamma

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

MacromoleculeName: Leucine-rich repeat serine/threonine-protein kinase 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 290.652188 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGSDYKDHDG DYKDHDIDYK DDDDKLGLEV LFQGPMASGS CQGCEEDEET LKKLIVRLNN VQEGKQIETL VQILEDLLVF TYSEHASKL FQGKNIHVPL LIVLDSYMRV ASVQQVGWSL LCKLIEVCPG TMQSLMGPQD VGNDWEVLGV HQLILKMLTV H NASVNLSV ...String:
MGSDYKDHDG DYKDHDIDYK DDDDKLGLEV LFQGPMASGS CQGCEEDEET LKKLIVRLNN VQEGKQIETL VQILEDLLVF TYSEHASKL FQGKNIHVPL LIVLDSYMRV ASVQQVGWSL LCKLIEVCPG TMQSLMGPQD VGNDWEVLGV HQLILKMLTV H NASVNLSV IGLKTLDLLL TSGKITLLIL DEESDIFMLI FDAMHSFPAN DEVQKLGCKA LHVLFERVSE EQLTEFVENK DY MILLSAL TNFKDEEEIV LHVLHCLHSL AIPCNNVEVL MSGNVRCYNI VVEAMKAFPM SERIQEVSCC LLHRLTLGNF FNI LVLNEV HEFVVKAVQQ YPENAALQIS ALSCLALLTE TIFLNQDLEE KNENQENDDE GEEDKLFWLE ACYKALTWHR KNKH VQEAA CWALNNLLMY QNSLHEKIGD EDGHFPAHRE VMLSMLMHSS SKEVFQASAN ALSTLLEQNV NFRKILLSKG IHLNV LELM QKHIHSPEVA ESGCKMLNHL FEGSNTSLDI MAAVVPKILT VMKRHETSLP VQLEALRAIL HFIVPGMPEE SREDTE FHH KLNMVKKQCF KNDIHKLVLA ALNRFIGNPG IQKCGLKVIS SIVHFPDALE MLSLEGAMDS VLHTLQMYPD DQEIQCL GL SLIGYLITKK NVFIGTGHLL AKILVSSLYR FKDVAEIQTK GFQTILAILK LSASFSKLLV HHSFDLVIFH QMSSNIME Q KDQQFLNLCC KCFAKVAMDD YLKNVMLERA CDQNNSIMVE CLLLLGADAN QAKEGSSLIC QVCEKESSPK LVELLLNSG SREQDVRKAL TISIGKGDSQ IISLLLRRLA LDVANNSICL GGFCIGKVEP SWLGPLFPDK TSNLRKQTNI ASTLARMVIR YQMKSAVEE GTASGSDGNF SEDVLSKFDE WTFIPDSSMD SVFAQSDDLD SEGSEGSFLV KKKSN(SEP)ISVG EFYRDAV LQ RCSPNLQRHS N(SEP)LGPIFDHE DLLKRKRKIL SSDDSLRSSK LQSHMRHSDS ISSLASEREY ITSLDLSANE LRDI DALSQ KCCISVHLEH LEKLELHQNA LTSFPQQLCE TLKSLTHLDL HSNKFTSFPS YLLKMSCIAN LDVSRNDIGP SVVLD PTVK CPTLKQFNLS YNQLSFVPEN LTDVVEKLEQ LILEGNKISG ICSPLRLKEL KILNLSKNHI SSLSENFLEA CPKVES FSA RMNFLAAMPF LPPSMTILKL SQNKFSCIPE AILNLPHLRS LDMSSNDIQY LPGPAHWKSL NLRELLFSHN QISILDL SE KAYLWSRVEK LHLSHNKLKE IPPEIGCLEN LTSLDVSYNL ELRSFPNEMG KLSKIWDLPL DELHLNFDFK HIGCKAKD I IRFLQQRLKK AVPYNRMKLM IVGNTGSGKT TLLQQLMKTK KSDLGMQSAT VGIDVKDWPI QIRDKRKRDL VLNVWDFAG REEFYSTHPH FMTQRALYLA VYDLSKGQAE VDAMKPWLFN IKARASSSPV ILVGTHLDVS DEKQRKACMS KITKELLNKR GFPAIRDYH FVNATEESDA LAKLRKTIIN ESLNFKIRDQ LVVGQLIPDC YVELEKIILS ERKNVPIEFP VIDRKRLLQL V RENQLQLD ENELPHAVHF LNESGVLLHF QDPALQLSDL YFVEPKWLCK IMAQILTVKV EGCPKHPKGI ISRRDVEKFL SK KRKFPKN YMSQYFKLLE KFQIALPIGE EYLLVPSSLS DHRPVIELPH CENSEIIIRL YEMPYFPMGF WSRLINRLLE ISP YMLSGR ERALRPNRMY WRQGIYLNWS PEAYCLVGSE VLDNHPESFL KITVPSCRKG CILLGQVVDH IDSLMEEWFP GLLE IDICG EGETLLKKWA LYSFNDGEEH QKILLDDLMK KAEEGDLLVN PDQPRLTIPI SQIAPDLILA DLPRNIMLNN DELEF EQAP EFLLGDGSFG SVYRAAYEGE EVAVKIFNKH TSLRLLRQEL VVLCHLHHPS LISLLAAGIR PRMLVMELAS KGSLDR LLQ QDKASLTRTL QHRIALHVAD GLRYLHSAMI IYRDLKPHNV LLFTLYPNAA IIAKIADYGI AQYCCRMGIK TSEGTPG FR APEVARGNVI YNQQADVYSF GLLLYDILTT GGRIVEGLKF PNEFDELEIQ GKLPDPVKEY GCAPWPMVEK LIKQCLKE N PQERPTSAQV FDILNSAELV CLTRRILLPK NVIVECMVAT HHNSRNASIW LGCGHTDRGQ LSFLDLNTEG YTSEEVADS RILCLALVHL PVEKESWIVS GTQSGTLLVI NTEDGKKRHT LEKMTDSVTC LYCNSFSKQS KQKNFLLVGT ADGKLAIFED KTVKLKGAA PLKILNIGNV STPLMCLSES TNSTERNVMW GGCGTKIFSF SNDFTIQKLI ETRTSQLFSY AAFSDSNIIT V VVDTALYI AKQNSPVVEV WDKKTEKLCG LIDCVHFLRE VMVKENKESK HKMSYSGRVK TLCLQKNTAL WIGTGGGHIL LL DLSTRRL IRVIYNFCNS VRVMMTAQLG SLKNVMLVLG YNRKNTEGTQ KQKEIQSCLT VWDINLPHEV QNLEKHIEVR KEL AEKMRR TSVE

UniProtKB: Leucine-rich repeat serine/threonine-protein kinase 2

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Macromolecule #3: GUANOSINE-5'-DIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 1 / Formula: GDP
Molecular weightTheoretical: 443.201 Da
Chemical component information

ChemComp-GDP:
GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying molecule*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.2 mg/mL
BufferpH: 8.3
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 60.8 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS TALOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.8 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7lhw

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.96 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 432285
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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