[English] 日本語
Yorodumi
- PDB-2zej: Structure of the ROC domain from the Parkinson's disease-associat... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2zej
TitleStructure of the ROC domain from the Parkinson's disease-associated leucine-rich repeat kinase 2 reveals a dimeric GTPase
ComponentsLeucine-rich repeat kinase 2LRRK2
KeywordsTRANSFERASE / Parkinson's Disease / LRRK2 / ROC / GTPase / ROCO / 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


organelle / 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 ...organelle / 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 / regulation of synaptic vesicle transport / negative regulation of late endosome to lysosome 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 / negative regulation of autophagosome assembly / regulation of dopamine receptor signaling pathway / 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 dendritic spine morphogenesis / regulation of protein kinase A signaling / multivesicular body, internal vesicle / striatum development / protein localization to mitochondrion / cellular response to dopamine / presynaptic cytosol / positive regulation of protein autoubiquitination / endoplasmic reticulum organization / Wnt signalosome / positive regulation of programmed cell death / GTP metabolic process / regulation of canonical Wnt signaling pathway / negative regulation of protein processing / syntaxin-1 binding / regulation of reactive oxygen species metabolic process / negative regulation of GTPase activity / regulation of locomotion / autolysosome / protein kinase A binding / exploration behavior / regulation of synaptic vesicle exocytosis / Golgi-associated vesicle / PTK6 promotes HIF1A stabilization / clathrin binding / negative regulation of macroautophagy / lysosome organization / regulation of mitochondrial fission / neuromuscular junction development / intracellular distribution of mitochondria / Golgi organization / positive regulation of nitric-oxide synthase biosynthetic process / locomotory exploration behavior / microvillus / Rho protein signal transduction / cellular response to organic cyclic compound / MAP kinase kinase kinase activity / canonical Wnt signaling pathway / regulation of signal transduction / positive regulation of protein kinase activity / cellular response to manganese ion / endoplasmic reticulum exit site / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / positive regulation of autophagy / JNK cascade / regulation of synaptic transmission, glutamatergic / excitatory postsynaptic potential / regulation of membrane potential / cellular response to starvation / dendrite cytoplasm / GTPase activator activity / mitochondrion organization / tubulin binding / SNARE binding / neuron projection morphogenesis / negative regulation of protein phosphorylation / negative regulation of protein binding / positive regulation of protein ubiquitination / regulation of autophagy / determination of adult lifespan / calcium-mediated signaling / mitochondrial membrane / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / peptidyl-threonine phosphorylation / regulation of protein stability
Similarity search - Function
ROC domain from the Parkinson's disease-associated leucine-rich repeat kinase 2 / 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 / small GTPase Rab1 family profile. / Leucine rich repeat / Leucine-rich repeat, typical subtype ...ROC domain from the Parkinson's disease-associated leucine-rich repeat kinase 2 / 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 / small GTPase Rab1 family profile. / 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 / WD40-repeat-containing domain superfamily / Alpha-Beta Plaits / 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 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / non-specific serine/threonine protein kinase / Leucine-rich repeat serine/threonine-protein kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 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
DepositionDec 13, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Leucine-rich repeat kinase 2
B: Leucine-rich repeat kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7786
Polymers42,8432
Non-polymers9354
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7850 Å2
ΔGint-81.5 kcal/mol
Surface area14510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.438, 44.404, 53.681
Angle α, β, γ (deg.)81.51, 69.00, 78.71
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Leucine-rich repeat kinase 2 / LRRK2 / Dardarin


Mass: 21421.732 Da / Num. of mol.: 2 / Fragment: ROC-GTPase domain, UNP residues 1333-1516
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LRRK2 / Plasmid: pSKB3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21goldDE3
References: UniProt: Q17RV3, UniProt: Q5S007*PLUS, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.46 %
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: 0.97948 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 21, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97948 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 23675 / % possible obs: 93.1 % / Redundancy: 4 % / Biso Wilson estimate: 29.1 Å2 / Rmerge(I) obs: 0.126 / Net I/σ(I): 16.9
Reflection shellResolution: 2→2.03 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 1.8 / Num. unique all: 793 / % possible all: 62.3

-
Processing

Software
NameVersionClassification
REFMAC5.3.0037refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2→38.8 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.924 / SU B: 8.66 / SU ML: 0.14 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.198 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25306 1192 5.1 %RANDOM
Rwork0.19874 ---
obs0.20156 22346 93.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.29 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å2-0.16 Å2-0.43 Å2
2---0.59 Å2-0.38 Å2
3---0.76 Å2
Refinement stepCycle: LAST / Resolution: 2→38.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2538 0 58 112 2708
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222601
X-RAY DIFFRACTIONr_angle_refined_deg2.1451.983530
X-RAY DIFFRACTIONr_dihedral_angle_1_deg15.9085317
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.98724.571105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.04515455
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3461511
X-RAY DIFFRACTIONr_chiral_restr0.270.2408
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021876
X-RAY DIFFRACTIONr_nbd_refined0.2120.21097
X-RAY DIFFRACTIONr_nbtor_refined0.3050.21725
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2165
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2020.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2220.28
X-RAY DIFFRACTIONr_mcbond_it1.2061.51634
X-RAY DIFFRACTIONr_mcangle_it1.73622556
X-RAY DIFFRACTIONr_scbond_it3.49731127
X-RAY DIFFRACTIONr_scangle_it4.6274.5972
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 46 -
Rwork0.222 1191 -
obs--67.34 %
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)
12.23970.9937-0.69751.6663-0.24840.8813-0.0109-0.2056-0.21760.0711-0.0122-0.05120.1104-0.02940.0231-0.14220.0392-0.0209-0.0961-0.06770.056529.40337.21444.793
22.34020.8869-0.78251.9717-0.56340.83580.0136-0.00480.0275-0.1842-0.0553-0.1414-0.06090.07710.0416-0.14520.0347-0.0028-0.1007-0.08650.036744.67549.96433.221
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1335 - 15073 - 175
2X-RAY DIFFRACTION2BB1336 - 15104 - 178

+
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