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- PDB-9c61: Crystal structure of the human LRRK2 WDR domain in complex with C... -

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Basic information

Entry
Database: PDB / ID: 9c61
TitleCrystal structure of the human LRRK2 WDR domain in complex with CACHE1193-26
ComponentsNon-specific serine/threonine protein kinase
KeywordsCYTOSOLIC PROTEIN / WD-repeat / WDR / LRRK2 / SGC
Function / homology
Function and homology information


GTP-dependent protein kinase activity / cell communication / regulation of signal transduction / protein autophosphorylation / non-specific serine/threonine protein kinase / protein phosphorylation / GTP binding / ATP binding / cytoplasm
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 / Small GTPase Rab domain profile. / 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. / WD40-repeat-containing domain superfamily / Protein kinase domain / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.6 Å
AuthorsZeng, H. / Dong, A. / Kutera, M. / Ilyassov, O. / Seitova, A. / Loppnau, P. / Schapira, M. / Arrowsmith, C.H. / Edwards, A.M. / Halabelian, L.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: To be published
Title: Crystal structure of the human LRRK2 WDR domain in complex with CACHE1193-26
Authors: Zeng, H. / Dong, A. / Kutera, M. / Ilyassov, O. / Seitova, A. / Loppnau, P. / Schapira, M. / Arrowsmith, C.H. / Edwards, A.M. / Halabelian, L.
History
DepositionJun 7, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Non-specific serine/threonine protein kinase
B: Non-specific serine/threonine protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,9666
Polymers87,2792
Non-polymers6874
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-6 kcal/mol
Surface area25770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.162, 103.064, 115.301
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 Non-specific serine/threonine protein kinase


Mass: 43639.406 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: Q17RV3, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-A1AUU / (4R)-4-[4-(5-fluoro-1H-indol-3-yl)piperidine-1-carbonyl]piperidin-2-one


Mass: 343.395 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H22FN3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 2 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.69 Å3/Da / Density % sol: 54.35 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris-HCl at pH 8.5, 1 M LiCl, 14% (w/v) polyethylene glycol (PEG) 6000 and 10% galactose

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 11, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 29052 / % possible obs: 96.9 % / Redundancy: 7.5 % / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.022 / Rrim(I) all: 0.061 / Χ2: 0.828 / Net I/σ(I): 9.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.6-2.647.40.90214250.7950.9410.350.970.72797.7
2.64-2.697.20.74614230.8840.9690.2910.8030.72597.7
2.69-2.7470.60713520.8760.9670.2420.6560.74891
2.74-2.87.60.50313500.9260.980.1930.540.7592
2.8-2.867.90.4114510.950.9870.1540.4390.76798.6
2.86-2.937.90.33314680.9670.9920.1250.3560.78899.2
2.93-380.28614590.9740.9930.1070.3060.79198.9
3-3.087.90.23314610.9850.9960.0880.2490.81898.6
3.08-3.177.80.17314750.9880.9970.0660.1850.8998.8
3.17-3.287.80.13114620.9930.9980.050.1410.92798.9
3.28-3.397.60.10814710.9920.9980.0420.1160.92298.9
3.39-3.537.50.08814690.9960.9990.0340.0940.94899.1
3.53-3.697.40.07314740.9970.9990.0280.0780.96398.3
3.69-3.887.10.06114550.9960.9990.0240.0660.97297.5
3.88-4.137.20.0513230.9970.9990.020.0540.94387.7
4.13-4.457.70.0415020.99910.0150.0430.85599.5
4.45-4.897.60.03514920.99910.0140.0380.82899
4.89-5.67.50.03215100.99910.0120.0340.77898.8
5.6-7.057.30.03215050.99910.0120.0340.7696.9
7.05-507.20.02315250.99910.0090.0250.66392.3

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
HKL-3000data scaling
REFMACphasing
HKL-3000data reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.6→47.05 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.908 / SU R Cruickshank DPI: 0.371 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.366 / SU Rfree Blow DPI: 0.252 / SU Rfree Cruickshank DPI: 0.256
RfactorNum. reflection% reflectionSelection details
Rfree0.24 2412 8.31 %RANDOM
Rwork0.199 ---
obs0.202 29020 96.7 %-
Displacement parametersBiso mean: 74.28 Å2
Baniso -1Baniso -2Baniso -3
1-13.3604 Å20 Å20 Å2
2---4.5118 Å20 Å2
3----8.8486 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: 1 / Resolution: 2.6→47.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4773 0 52 44 4869
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014895HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.26649HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1652SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes818HARMONIC5
X-RAY DIFFRACTIONt_it4895HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.16
X-RAY DIFFRACTIONt_other_torsion18.56
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion686SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5201SEMIHARMONIC4
LS refinement shellResolution: 2.6→2.61 Å
RfactorNum. reflection% reflection
Rfree0.3226 -8.78 %
Rwork0.2468 530 -
obs--85.5 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.64790.9252-0.10012.60160.15751.4242-0.15150.36080.2437-0.19290.20890.0752-0.03830.1096-0.0574-0.12730.0241-0.0461-0.1-0.032-0.1324-18.146-12.8018.3135
21.9531.23941.07023.86311.10512.112-0.11370.6264-0.3696-0.40710.3907-0.4295-0.08930.4989-0.277-0.2556-0.07810.1105-0.0412-0.1257-0.14724.294611.67514.8265
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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