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- PDB-6dlo: Crystal structure of LRRK2 WD40 domain dimer -

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Basic information

Entry
Database: PDB / ID: 6dlo
TitleCrystal structure of LRRK2 WD40 domain dimer
ComponentsLeucine-rich repeat serine/threonine-protein kinase 2
KeywordsCYTOSOLIC PROTEIN / Parkinson's disease / LRRK2 / WD40
Function / homology
Function and homology information


peroxidase inhibitor activity / caveola neck / negative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation / negative regulation of protein processing involved in protein targeting to mitochondrion / Wnt signalosome assembly / beta-catenin destruction complex binding / regulation of branching morphogenesis of a nerve / regulation of kidney size / regulation of neuron maturation / tangential migration from the subventricular zone to the olfactory bulb ...peroxidase inhibitor activity / caveola neck / negative regulation of thioredoxin peroxidase activity by peptidyl-threonine phosphorylation / negative regulation of protein processing involved in protein targeting to mitochondrion / Wnt signalosome assembly / beta-catenin destruction complex binding / regulation of branching morphogenesis of a nerve / regulation of kidney size / regulation of neuron maturation / tangential migration from the subventricular zone to the olfactory bulb / protein localization to endoplasmic reticulum exit site / GTP-dependent protein kinase activity / regulation of neuroblast proliferation / regulation of ER to Golgi vesicle-mediated transport / negative regulation of late endosome to lysosome transport / regulation of synaptic vesicle transport / regulation of mitochondrial depolarization / negative regulation of protein targeting to mitochondrion / positive regulation of dopamine receptor signaling pathway / regulation of lysosomal lumen pH / regulation of CAMKK-AMPK signaling cascade / amphisome / mitochondrion localization / cytoplasmic side of mitochondrial outer membrane / co-receptor binding / regulation of retrograde transport, endosome to Golgi / negative regulation of excitatory postsynaptic potential / regulation of dopamine receptor signaling pathway / negative regulation of autophagosome assembly / positive regulation of microglial cell activation / neuron projection arborization / positive regulation of synaptic vesicle endocytosis / JUN kinase kinase kinase activity / olfactory bulb development / regulation of protein kinase A signaling / multivesicular body, internal vesicle / striatum development / regulation of dendritic spine morphogenesis / protein localization to mitochondrion / cellular response to dopamine / presynaptic cytosol / positive regulation of protein autoubiquitination / endoplasmic reticulum organization / positive regulation of programmed cell death / Wnt signalosome / regulation of canonical Wnt signaling pathway / GTP metabolic process / negative regulation of protein processing / syntaxin-1 binding / regulation of reactive oxygen species metabolic process / negative regulation of GTPase activity / exploration behavior / autolysosome / protein kinase A binding / regulation of locomotion / Golgi-associated vesicle / neuromuscular junction development / regulation of synaptic vesicle exocytosis / PTK6 promotes HIF1A stabilization / clathrin binding / negative regulation of macroautophagy / regulation of mitochondrial fission / lysosome organization / intracellular distribution of mitochondria / positive regulation of nitric-oxide synthase biosynthetic process / locomotory exploration behavior / Golgi organization / endoplasmic reticulum exit site / microvillus / Rho protein signal transduction / MAP kinase kinase kinase activity / positive regulation of protein kinase activity / canonical Wnt signaling pathway / cellular response to manganese ion / positive regulation of autophagy / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / JNK cascade / regulation of synaptic transmission, glutamatergic / excitatory postsynaptic potential / dendrite cytoplasm / cellular response to starvation / tubulin binding / mitochondrion organization / GTPase activator activity / neuron projection morphogenesis / SNARE binding / negative regulation of protein phosphorylation / negative regulation of protein binding / positive regulation of protein ubiquitination / regulation of autophagy / regulation of membrane potential / determination of adult lifespan / mitochondrial membrane / calcium-mediated signaling / peptidyl-threonine phosphorylation / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / positive regulation of MAP kinase activity / regulation of protein stability / protein localization / trans-Golgi network
Similarity search - Function
C-terminal of Roc (COR) domain / C-terminal of Roc, COR, 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. ...C-terminal of Roc (COR) domain / C-terminal of Roc, COR, 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 / WD40-repeat-containing domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 Å
AuthorsZhang, P. / Ru, H. / Wang, L. / Wu, H.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2019
Title: Crystal structure of the WD40 domain dimer of LRRK2.
Authors: Zhang, P. / Fan, Y. / Ru, H. / Wang, L. / Magupalli, V.G. / Taylor, S.S. / Alessi, D.R. / Wu, H.
History
DepositionJun 2, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Feb 13, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Leucine-rich repeat serine/threonine-protein kinase 2
A: Leucine-rich repeat serine/threonine-protein kinase 2


Theoretical massNumber of molelcules
Total (without water)87,3392
Polymers87,3392
Non-polymers00
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-4 kcal/mol
Surface area26900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.293, 103.590, 112.664
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 43669.500 Da / Num. of mol.: 2 / Fragment: WD40 domain residues 2142-2527
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
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.57 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris-HCl at pH 8.5, 1 M LiCl, 16% polyethylene glycol (PEG) 6000, and 10% additive of 30% galactose

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.61→103.07 Å / Num. obs: 28401 / % possible obs: 99.1 % / Redundancy: 3.5 % / Net I/σ(I): 14.6
Reflection shellResolution: 2.61→2.73 Å

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
XDSdata reduction
XDSdata scaling
AutoSolphasing
RefinementResolution: 2.7→76.256 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 0.03 / Phase error: 26.97
RfactorNum. reflection% reflection
Rfree0.2753 2004 8.29 %
Rwork0.2342 --
obs0.2375 24181 92.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.7→76.256 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4825 0 0 66 4891
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024888
X-RAY DIFFRACTIONf_angle_d0.6126601
X-RAY DIFFRACTIONf_dihedral_angle_d10.1982920
X-RAY DIFFRACTIONf_chiral_restr0.047806
X-RAY DIFFRACTIONf_plane_restr0.003803
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.76760.44221430.37591271X-RAY DIFFRACTION77
2.7676-2.84240.41431040.34111354X-RAY DIFFRACTION79
2.8424-2.9260.36251250.30431386X-RAY DIFFRACTION82
2.926-3.02050.3111420.2891448X-RAY DIFFRACTION87
3.0205-3.12840.32071240.25731533X-RAY DIFFRACTION89
3.1284-3.25370.27941490.25081561X-RAY DIFFRACTION93
3.2537-3.40180.26971420.25261598X-RAY DIFFRACTION94
3.4018-3.58110.2961510.22881658X-RAY DIFFRACTION97
3.5811-3.80550.28241430.21721669X-RAY DIFFRACTION98
3.8055-4.09930.23771530.20791682X-RAY DIFFRACTION99
4.0993-4.51180.22121510.18111727X-RAY DIFFRACTION99
4.5118-5.16450.21081510.17341716X-RAY DIFFRACTION99
5.1645-6.50620.24621600.21871736X-RAY DIFFRACTION99
6.5062-76.2860.26481660.24631838X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 3.3248 Å / Origin y: -0.1283 Å / Origin z: 11.1416 Å
111213212223313233
T0.1554 Å2-0.0161 Å20.0386 Å2-0.1674 Å2-0.0539 Å2--0.1484 Å2
L1.0813 °21.1511 °20.2753 °2-1.2419 °20.3451 °2--0.4312 °2
S-0.1821 Å °0.4606 Å °0.0369 Å °-0.2333 Å °0.2405 Å °-0.0792 Å °-0.0757 Å °0.1733 Å °-0.0486 Å °
Refinement TLS groupSelection details: all

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