[English] 日本語
Yorodumi
- PDB-3d6t: Structure of the ROC domain from the Parkinson's disease-associat... -

+
Open data


ID or keywords:

Loading...

-
Basic information

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


regulation of neuron maturation / caveola neck / : / beta-catenin destruction complex binding / regulation of branching morphogenesis of a nerve / Wnt signalosome assembly / negative regulation of motile cilium assembly / regulation of kidney size / regulation of cell projection organization / regulation of dopamine receptor signaling pathway ...regulation of neuron maturation / caveola neck / : / beta-catenin destruction complex binding / regulation of branching morphogenesis of a nerve / Wnt signalosome assembly / negative regulation of motile cilium assembly / regulation of kidney size / regulation of cell projection organization / regulation of dopamine receptor signaling pathway / tangential migration from the subventricular zone to the olfactory bulb / regulation of ER to Golgi vesicle-mediated transport / GTP-dependent protein kinase activity / regulation of SNARE complex assembly / regulation of neuroblast proliferation / protein localization to endoplasmic reticulum exit site / negative regulation of late endosome to lysosome transport / regulation of mitochondrial depolarization / : / peroxidase inhibitor activity / positive regulation of dopamine receptor signaling pathway / amphisome / regulation of synaptic vesicle transport / : / regulation of CAMKK-AMPK signaling cascade / negative regulation of autophagosome assembly / co-receptor binding / positive regulation of microglial cell activation / olfactory bulb development / regulation of retrograde transport, endosome to Golgi / negative regulation of GTPase activity / cellular response to curcumin / striatum development / regulation of locomotion / positive regulation of synaptic vesicle endocytosis / JUN kinase kinase kinase activity / cytoplasmic side of mitochondrial outer membrane / negative regulation of excitatory postsynaptic potential / regulation of cAMP/PKA signal transduction / multivesicular body, internal vesicle / endoplasmic reticulum organization / neuron projection arborization / mitochondrion localization / regulation of dendritic spine morphogenesis / protein localization to mitochondrion / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / cellular response to dopamine / negative regulation of protein processing / positive regulation of protein autoubiquitination / Wnt signalosome / exploration behavior / GTP metabolic process / regulation of reactive oxygen species metabolic process / regulation of canonical Wnt signaling pathway / lysosome organization / syntaxin-1 binding / positive regulation of programmed cell death / negative regulation of macroautophagy / PTK6 promotes HIF1A stabilization / Golgi-associated vesicle / clathrin binding / Golgi organization / regulation of synaptic vesicle exocytosis / regulation of mitochondrial fission / intracellular distribution of mitochondria / Lewy body / protein kinase A binding / canonical Wnt signaling pathway / microvillus / neuromuscular junction development / locomotory exploration behavior / autolysosome / endoplasmic reticulum exit site / MAP kinase kinase kinase activity / JNK cascade / regulation of synaptic vesicle endocytosis / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / Rho protein signal transduction / regulation of synaptic transmission, glutamatergic / determination of adult lifespan / presynaptic cytosol / cellular response to manganese ion / neuron projection morphogenesis / phagocytic vesicle / positive regulation of autophagy / dendrite cytoplasm / excitatory postsynaptic potential / positive regulation of protein ubiquitination / cellular response to starvation / regulation of autophagy / GTPase activator activity / calcium-mediated signaling / mitochondrion organization / SNARE binding / negative regulation of neuron projection development / cellular response to reactive oxygen species / regulation of protein stability / trans-Golgi network / regulation of membrane potential / tubulin binding
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 ...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 / Leucine-rich repeat domain superfamily / Rab subfamily of small GTPases / 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 / Serine/Threonine protein kinases, catalytic domain / WD40-repeat-containing domain superfamily / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more