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- PDB-3d6t: Structure of the ROC domain from the Parkinson's disease-associat... -

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Entry
Database: PDB / ID: 3d6t
TitleStructure of the ROC domain from the Parkinson's disease-associated leucine-rich repeat kinase 2 reveals a dimeric GTPase
ComponentsLeucine-rich repeat serine/threonine-protein kinase 2
KeywordsTRANSFERASE / parkinson's disease / LRRK2 / Roc / Roco / GTPase / Kinase / ATP-binding / Disease Mutation / GTP-binding / GTPase activation / Leucine-rich repeat / membrane / nucleotide-binding / parkinson disease / serine/threonine-protein kinase
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 / regulation of canonical Wnt signaling pathway / GTP metabolic process / 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 / Golgi organization / intracellular distribution of mitochondria / microvillus / 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 / regulation of membrane potential / cellular response to reactive oxygen species / 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
ROC domain from the Parkinson's disease-associated leucine-rich repeat kinase 2 / : / : / : / LRRK2 ARM repeat / LRRK2 ANK repeat / LRRK2 beta propeller / : / C-terminal of Roc, COR-B domain / C-terminal of Roc (COR) domain ...ROC domain from the Parkinson's disease-associated leucine-rich repeat kinase 2 / : / : / : / 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 / P-loop containing nucleotide triphosphate hydrolases / Alpha-Beta Plaits / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Leucine-rich repeat serine/threonine-protein kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.43 Å
AuthorsDeng, J.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Structure of the ROC domain from the Parkinson's disease-associated leucine-rich repeat kinase 2 reveals a dimeric GTPase
Authors: Deng, J. / Lewis, P.A. / Greggio, E. / Sluch, E. / Beilina, A. / Cookson, M.R.
History
DepositionMay 20, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Advisory / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_unobs_or_zero_occ_atoms / software
Item: _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id ..._entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_strain / _software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 28, 2018Group: Structure summary / Category: struct_keywords / Item: _struct_keywords.text
Revision 1.4Nov 6, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2703
Polymers19,8031
Non-polymers4682
Water1086
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Leucine-rich repeat serine/threonine-protein kinase 2
hetero molecules

B: Leucine-rich repeat serine/threonine-protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5416
Polymers39,6062
Non-polymers9354
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area6630 Å2
ΔGint-42.7 kcal/mol
Surface area13090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.919, 53.167, 42.736
Angle α, β, γ (deg.)90.00, 112.76, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 19802.953 Da / Num. of mol.: 1 / Fragment: Miro domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LRRK2, PARK8 / Plasmid: PSKB3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21GOLDDE3
References: UniProt: Q5S007, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.85 Å3/Da / Density % sol: 33.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 30% PEG 4000, 100mM MgCl2, 0.1M Tris, 5mM GTP, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 21, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.43→21.09 Å / Num. obs: 5109
Reflection scaleGroup code: 1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
RefinementResolution: 2.43→21.09 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.861 / SU B: 25.808 / SU ML: 0.288 / TLS residual ADP flag: LIKELY RESIDUAL / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflection
Rfree0.307 230 4.5 %
Rwork0.211 --
obs0.216 5109 93 %
Solvent computationSolvent model: MASK
Displacement parametersBiso mean: 33.24 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20.04 Å2
2---0.48 Å20 Å2
3---0.59 Å2
Refinement stepCycle: LAST / Resolution: 2.43→21.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms994 0 29 6 1029
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0221023
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3421.9951383
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3025116
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.60222.89538
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.90215168
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.39155
X-RAY DIFFRACTIONr_chiral_restr0.1130.2161
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02717
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.290.2378
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3390.2667
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.231
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2280.246
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2560.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8871.5633
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.4192977
X-RAY DIFFRACTIONr_scbond_it2.33467
X-RAY DIFFRACTIONr_scangle_it3.3754.5406
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.43→2.5 Å
RfactorNum. reflection% reflection
Rfree0.541 15 -
Rwork0.304 238 -
obs--65.21 %
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)
138.3732-16.6866-7.17220.894-4.68625.80730.2686-1.17780.15840.53220.01980.5494-1.07410.0109-0.28830.1118-0.0770.01040.0893-0.14230.175831.8868-8.705429.009
27.6445-3.7281.443511.57050.35360.38730.02410.0897-0.01920.1579-0.1615-0.2721-0.3169-0.01160.13740.12210.05280.02140.1616-0.05770.132841.1984-16.017623.8143
33.7869-0.73855.22935.6450.2947.535-0.2819-0.2808-0.35330.76050.18470.75990.0723-0.71280.09720.10570.02130.16520.13350.03960.178230.186-16.498730.517
410.26917.4708-12.55045.4351-9.130415.3384-0.2125-0.4444-1.21220.1242-0.40850.3411-0.22070.34680.6210.0631-0.06810.04450.1963-0.06530.166132.669-12.414422.9618
513.65894.5987-7.122329.306834.486952.72570.19251.59410.9887-1.47051.2153-1.4178-1.25121.3216-1.40780.04860.01680.10590.1514-0.01210.171737.4677-7.925515.4981
65.6023-4.16973.790318.40982.45484.3829-0.06310.2440.64380.5860.01680.10290.3653-0.46530.04630.0416-0.01130.01760.07760.08170.231231.3894-1.252414.7079
715.58139.28083.65385.67683.16447.413-0.62250.25530.7466-0.3679-0.15820.5295-0.41820.60560.78070.08180.00740.00710.08460.07780.30924.5734-1.252710.8083
810.59492.42150.90964.8581.89420.73870.35340.1070.73710.0335-0.22620.92630.1043-0.047-0.12720.1135-0.0279-0.01540.12390.00630.15187.6025-11.251412.5676
93.76237.9333-2.839420.007-1.20079.1305-0.40190.7914-0.4284-0.46560.29230.57990.3732-0.34940.10960.08840.00640.13410.042-0.06930.35272.0613-6.271817.5588
101.68470.7692-0.01315.11091.14923.49960.00680.14650.47-0.32660.1610.0995-0.3348-0.2177-0.16780.07680.0137-0.00020.09260.05920.155811.926-3.161613.0041
118.49479.77234.004912.13326.25814.946-0.2981-0.23160.6055-1.47810.16611.846-0.6227-0.47520.1320.0932-0.0057-0.00080.0622-0.00890.1655-1.0441-11.39899.227
125.4349-1.0352-2.630713.8121-0.10459.2836-0.35870.80040.1447-1.51630.24680.3236-0.5531-0.52030.1119-0.0002-0.1017-0.13510.07210.11040.20858.4244-2.7435.7705
1310.44823.3272-1.76945.13340.31763.7085-0.37210.762-0.4408-1.02710.1653-0.14970.371-0.29610.20680.27640.0114-0.0350.0443-0.0365-0.024810.9963-17.42012.806
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1BA1335 - 13391 - 5
2X-RAY DIFFRACTION2BA1340 - 13516 - 17
3X-RAY DIFFRACTION3BA1353 - 139019 - 56
4X-RAY DIFFRACTION4BA1392 - 139658 - 62
5X-RAY DIFFRACTION5BA1397 - 140163 - 67
6X-RAY DIFFRACTION6BA1402 - 140768 - 73
7X-RAY DIFFRACTION7BA1408 - 141474 - 80
8X-RAY DIFFRACTION8BA1415 - 142281 - 88
9X-RAY DIFFRACTION9BA1423 - 143389 - 99
10X-RAY DIFFRACTION10BA1434 - 1453100 - 119
11X-RAY DIFFRACTION11BA1454 - 1474120 - 140
12X-RAY DIFFRACTION12BA1478 - 1486144 - 152
13X-RAY DIFFRACTION13BA1487 - 1505153 - 171

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