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- EMDB-21250: Cryo-EM structure of the C-terminal half of the Parkinson's Disea... -

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Entry
Database: EMDB / ID: EMD-21250
TitleCryo-EM structure of the C-terminal half of the Parkinson's Disease-linked protein Leucine Rich Repeat Kinase 2 (LRRK2)
Map data3.8A signal subtracted locally filtered cryo-EM map of C-terminal half of Leucine Rich Repeat Kinase 2 (LRRK2)
Sample
  • Complex: The C-terminal half of the Leucine Rich Repeat Kinase 2 (LRRK2) protein.
    • Protein or peptide: Leucine-rich repeat serine/threonine-protein kinase 2
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsKinase / GTPase / SIGNALING PROTEIN
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 / regulation of CAMKK-AMPK signaling cascade / co-receptor binding / negative regulation of GTPase activity / 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 / 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 / GTP metabolic process / regulation of canonical Wnt signaling pathway / 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 / 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 / negative regulation of Notch signaling pathway / MAP kinase kinase kinase activity / regulation of synaptic vesicle endocytosis / canonical Wnt signaling pathway / regulation of synaptic transmission, glutamatergic / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / presynaptic cytosol / Rho protein signal transduction / neuron projection morphogenesis / phagocytic vesicle / cellular response to manganese ion / JNK cascade / positive regulation of autophagy / dendrite cytoplasm / tubulin binding / GTPase activator activity / cellular response to starvation / positive regulation of protein ubiquitination / SNARE binding / determination of adult lifespan / cellular response to reactive oxygen species / regulation of membrane potential / excitatory postsynaptic potential / mitochondrion organization / trans-Golgi network / calcium-mediated signaling / regulation of protein stability / autophagy / small GTPase binding / mitochondrial membrane / endocytosis
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 / 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
Leucine-rich repeat serine/threonine-protein kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsLeschziner A / Deniston C / Lahiri I
Funding support United States, 3 items
OrganizationGrant numberCountry
Michael J. Fox Foundation11425 United States
Michael J. Fox Foundation11425.02 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM107214 United States
CitationJournal: Nature / Year: 2020
Title: Structure of LRRK2 in Parkinson's disease and model for microtubule interaction.
Authors: C K Deniston / J Salogiannis / S Mathea / D M Snead / I Lahiri / M Matyszewski / O Donosa / R Watanabe / J Böhning / A K Shiau / S Knapp / E Villa / S L Reck-Peterson / A E Leschziner /
Abstract: Leucine-rich repeat kinase 2 (LRRK2) is the most commonly mutated gene in familial Parkinson's disease and is also linked to its idiopathic form. LRRK2 has been proposed to function in membrane ...Leucine-rich repeat kinase 2 (LRRK2) is the most commonly mutated gene in familial Parkinson's disease and is also linked to its idiopathic form. LRRK2 has been proposed to function in membrane trafficking and colocalizes with microtubules. Despite the fundamental importance of LRRK2 for understanding and treating Parkinson's disease, structural information on the enzyme is limited. Here we report the structure of the catalytic half of LRRK2, and an atomic model of microtubule-associated LRRK2 built using a reported cryo-electron tomography in situ structure. We propose that the conformation of the LRRK2 kinase domain regulates its interactions with microtubules, with a closed conformation favouring oligomerization on microtubules. We show that the catalytic half of LRRK2 is sufficient for filament formation and blocks the motility of the microtubule-based motors kinesin 1 and cytoplasmic dynein 1 in vitro. Kinase inhibitors that stabilize an open conformation relieve this interference and reduce the formation of LRRK2 filaments in cells, whereas inhibitors that stabilize a closed conformation do not. Our findings suggest that LRRK2 can act as a roadblock for microtubule-based motors and have implications for the design of therapeutic LRRK2 kinase inhibitors.
History
DepositionJan 29, 2020-
Header (metadata) releaseAug 26, 2020-
Map releaseAug 26, 2020-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0267
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  • Surface view colored by radius
  • Surface level: 0.0267
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  • Surface view with fitted model
  • Atomic models: PDB-6vno
  • Surface level: 0.05
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  • Surface view with fitted model
  • Atomic models: PDB-6vp6
  • Surface level: 0.03
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  • Surface view with fitted model
  • Atomic models: PDB-6vp7
  • Surface level: 0.06
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  • Surface view with fitted model
  • Atomic models: PDB-6vp8
  • Surface level: 0.0267
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6vno
  • Imaged by Jmol
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6vp6
  • Imaged by Jmol
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6vp7
  • Imaged by Jmol
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6vp8
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Movie viewer
Structure viewerEM map:
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Supplemental images

emd_21250.png

Downloads & links

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Map

FileDownload / File: emd_21250.map.gz / Format: CCP4 / Size: 172.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3.8A signal subtracted locally filtered cryo-EM map of C-terminal half of Leucine Rich Repeat Kinase 2 (LRRK2)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 356 pix.
= 380.92 Å		1.07 Å/pix.
x 356 pix.
= 380.92 Å		1.07 Å/pix.
x 356 pix.
= 380.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0267 / Movie #1: 0.0267
Minimum - Maximum-0.032042872 - 0.0754334
Average (Standard dev.)0.00008440901 (±0.0022088308)
SymmetrySpace group: 0
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions356356356
Spacing356356356
CellA=B=C: 380.92 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z356356356
origin x/y/z0.0000.0000.000
length x/y/z380.920380.920380.920
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS356356356
D min/max/mean-0.0320.0750.000

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Supplemental data

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Additional map: 3.47A C3 symmetric locally filtered cryo-EM map of...

Fileemd_21250_additional_1.map
Annotation3.47A C3 symmetric locally filtered cryo-EM map of C-terminal half of Leucine Rich Repeat Kinase 2 (LRRK2).
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Half map 1 of C3 symmetric map

Fileemd_21250_additional_2.map
AnnotationHalf map 1 of C3 symmetric map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Additional map: Half map 2 of C3 symmetric map

Fileemd_21250_additional_3.map
AnnotationHalf map 2 of C3 symmetric map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1 of signal subtracted map

Fileemd_21250_half_map_1.map
AnnotationHalf map 1 of signal subtracted map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2 of signal subtracted map

Fileemd_21250_half_map_2.map
AnnotationHalf map 2 of signal subtracted map
Projections & Slices
AxesZYX

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Sample components

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Entire : The C-terminal half of the Leucine Rich Repeat Kinase 2 (LRRK2) p...

EntireName: The C-terminal half of the Leucine Rich Repeat Kinase 2 (LRRK2) protein.
Components
  • Complex: The C-terminal half of the Leucine Rich Repeat Kinase 2 (LRRK2) protein.
    • Protein or peptide: Leucine-rich repeat serine/threonine-protein kinase 2
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: The C-terminal half of the Leucine Rich Repeat Kinase 2 (LRRK2) p...

SupramoleculeName: The C-terminal half of the Leucine Rich Repeat Kinase 2 (LRRK2) protein.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: C-terminal half runs from residue 1327-2527.
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 137 KDa

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

MacromoleculeName: Leucine-rich repeat serine/threonine-protein kinase 2 / type: protein_or_peptide / ID: 1 / Details: C-terminal residues 1330-2527 / Number of copies: 1 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 136.943609 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: KKAVPYNRMK LMIVGN(TPO)GSG KTTLLQQLMK TKKSDLGMQS ATVGIDVKDW PIQIRDKRKR DLVLNVWDFA GREEFY STH PHFMTQRALY LAVYDLSKGQ AEVDAMKPWL FNIKARASSS PVILVGTHLD VSDEKQRKAC MSKITKELLN KRGFPAI RD YHFVNATEES ...String:
KKAVPYNRMK LMIVGN(TPO)GSG KTTLLQQLMK TKKSDLGMQS ATVGIDVKDW PIQIRDKRKR DLVLNVWDFA GREEFY STH PHFMTQRALY LAVYDLSKGQ AEVDAMKPWL FNIKARASSS PVILVGTHLD VSDEKQRKAC MSKITKELLN KRGFPAI RD YHFVNATEES DALAKLRKTI INESLNFKIR DQLVVGQLIP DCYVELEKII LSERKNVPIE FPVIDRKRLL QLVRENQL Q LDENELPHAV HFLNESGVLL HFQDPALQLS DLYFVEPKWL CKIMAQILTV KVEGCPKHPK GIISRRDVEK FLSKKRKFP KNYMSQYFKL LEKFQIALPI GEEYLLVPSS LSDHRPVIEL PHCENSEIII RLYEMPYFPM GFWSRLINRL LEISPYMLSG RERALRPNR MYWRQGIYLN WSPEAYCLVG SEVLDNHPES FLKITVPSCR KGCILLGQVV DHIDSLMEEW FPGLLEIDIC G EGETLLKK WALYSFNDGE EHQKILLDDL MKKAEEGDLL VNPDQPRLTI PISQIAPDLI LADLPRNIML NNDELEFEQA PE FLLGDGS FGSVYRAAYE GEEVAVKIFN KHTSLRLLRQ ELVVLCHLHH PSLISLLAAG IRPRMLVMEL ASKGSLDRLL QQD KASLTR TLQHRIALHV ADGLRYLHSA MIIYRDLKPH NVLLFTLYPN AAIIAKIADY GIAQYCCRMG IKTSEGTPGF RAPE VARGN VIYNQQADVY SFGLLLYDIL TTGGRIVEGL KFPNEFDELE IQGKLPDPVK EYGCAPWPMV EKLIKQCLKE NPQER PTSA QVFDILNSAE LVCLTRRILL PKNVIVECMV ATHHNSRNAS IWLGCGHTDR GQLSFLDLNT EGYTSEEVAD SRILCL ALV HLPVEKESWI VSGTQSGTLL VINTEDGKKR HTLEKMTDSV TCLYCNSFSK QSKQKNFLLV GTADGKLAIF EDKTVKL KG AAPLKILNIG NVSTPLMCLS ESTNSTERNV MWGGCGTKIF SFSNDFTIQK LIETRTSQLF SYAAFSDSNI ITVVVDTA L YIAKQNSPVV EVWDKKTEKL CGLIDCVHFL REVMVKENKE SKHKMSYSGR VKTLCLQKNT ALWIGTGGGH ILLLDLSTR RLIRVIYNFC NSVRVMMTAQ LGSLKNVMLV LGYNRKNTEG TQKQKEIQSC LTVWDINLPH EVQNLEKHIE VRKELAEKMR RTSVE

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

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Macromolecule #2: GUANOSINE-5'-DIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / 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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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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

Concentration0.5 mg/mL
BufferpH: 7.4
Component:
ConcentrationNameFormula
20.0 mMHEPES
80.0 mMNaCl
0.5 mMTCEP
5.0 %Glycerol
2.5 mMMgCl2
20.0 uMGDP
GridModel: Quantifoil, UltrAuFoil, R1.2/1.3 / Material: GOLD / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK II
Details4uM concentration

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF 2002
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 3826 / Average exposure time: 8.0 sec. / Average electron dose: 6.65 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 836956
Startup modelType of model: OTHER
Details: Generated initial models from ab initio refinement in Cryosparc.
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software:
Namedetails
RELION (ver. 3)C1
cryoSPARC (ver. 2)C3

Details: For the signal subtracted map, 105,787 (tripled) particles went into the final map that achieved 3.8A resolution.
Number images used: 70953
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software: (Name: RELION (ver. 3), cryoSPARC (ver. 2))
Details: Signal subtracted map was generated in Relion3. The C3 map however was created in Cryosparc 2.
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software: (Name: RELION (ver. 3), cryoSPARC (ver. 2))
Details: Signal subtracted map was generated in Relion3. The C3 map however was created in Cryosparc 2.
FSC plot (resolution estimation)

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