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- PDB-2zeq: Crystal structure of ubiquitin-like domain of murine Parkin -

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Basic information

Entry
Database: PDB / ID: 2zeq
TitleCrystal structure of ubiquitin-like domain of murine Parkin
ComponentsE3 ubiquitin-protein ligase parkin
KeywordsLIGASE / Parkin / ubiquitin-like domain / Alternative splicing / Cell junction / Cell projection / Cytoplasm / Endoplasmic reticulum / Membrane / Metal-binding / Nucleus / Postsynaptic cell membrane / S-nitrosylation / Synapse / Ubl conjugation / Ubl conjugation pathway / Zinc / Zinc-finger
Function / homology
Function and homology information


positive regulation of neurotransmitter uptake / negative regulation of endoplasmic reticulum stress-induced neuron intrinsic apoptotic signaling pathway / mitochondrion-derived vesicle / negative regulation of spontaneous neurotransmitter secretion / negative regulation of intralumenal vesicle formation / regulation protein catabolic process at presynapse / Josephin domain DUBs / PINK1-PRKN Mediated Mitophagy / negative regulation of exosomal secretion / mitochondrion to lysosome vesicle-mediated transport ...positive regulation of neurotransmitter uptake / negative regulation of endoplasmic reticulum stress-induced neuron intrinsic apoptotic signaling pathway / mitochondrion-derived vesicle / negative regulation of spontaneous neurotransmitter secretion / negative regulation of intralumenal vesicle formation / regulation protein catabolic process at presynapse / Josephin domain DUBs / PINK1-PRKN Mediated Mitophagy / negative regulation of exosomal secretion / mitochondrion to lysosome vesicle-mediated transport / Regulation of necroptotic cell death / Aggrephagy / type 2 mitophagy / negative regulation of actin filament bundle assembly / negative regulation of mitochondrial fusion / Parkin-FBXW7-Cul1 ubiquitin ligase complex / free ubiquitin chain polymerization / positive regulation of protein linear polyubiquitination / negative regulation by host of viral genome replication / RBR-type E3 ubiquitin transferase / F-box domain binding / positive regulation of mitochondrial fusion / regulation of cellular response to oxidative stress / regulation of dopamine metabolic process / regulation of neurotransmitter secretion / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / dopaminergic synapse / positive regulation of dendrite extension / protein K6-linked ubiquitination / positive regulation of protein localization to membrane / autophagy of mitochondrion / norepinephrine metabolic process / cellular response to toxic substance / positive regulation of type 2 mitophagy / protein localization to mitochondrion / synaptic transmission, dopaminergic / negative regulation of JNK cascade / mitochondrial fission / positive regulation of tumor necrosis factor-mediated signaling pathway / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / Antigen processing: Ubiquitination & Proteasome degradation / aggresome assembly / protein K11-linked ubiquitination / ubiquitin conjugating enzyme binding / regulation of mitochondrion organization / aggresome / positive regulation of mitochondrial fission / dopamine uptake involved in synaptic transmission / ubiquitin-specific protease binding / negative regulation of release of cytochrome c from mitochondria / startle response / dopamine metabolic process / phospholipase binding / regulation of synaptic vesicle endocytosis / cullin family protein binding / negative regulation of reactive oxygen species metabolic process / protein K63-linked ubiquitination / protein monoubiquitination / negative regulation of insulin secretion / protein K48-linked ubiquitination / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / protein autoubiquitination / mitophagy / Hsp70 protein binding / tubulin binding / response to endoplasmic reticulum stress / regulation of mitochondrial membrane potential / adult locomotory behavior / ubiquitin binding / learning / synaptic transmission, glutamatergic / PDZ domain binding / mitochondrion organization / locomotory behavior / G protein-coupled receptor binding / modulation of chemical synaptic transmission / negative regulation of canonical Wnt signaling pathway / protein catabolic process / protein destabilization / beta-catenin binding / kinase binding / histone deacetylase binding / neuron cellular homeostasis / protein polyubiquitination / transcription corepressor activity / ubiquitin protein ligase activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / presynapse / actin binding / ubiquitin-dependent protein catabolic process / negative regulation of neuron apoptotic process / response to oxidative stress / proteasome-mediated ubiquitin-dependent protein catabolic process / mitochondrial outer membrane / positive regulation of canonical NF-kappaB signal transduction / neuron projection / postsynaptic density / regulation of autophagy / protein stabilization / nuclear speck
Similarity search - Function
: / E3 ubiquitin-protein ligase parkin / RING/Ubox-like zinc-binding domain / Parkin, RING/Ubox like zinc-binding domain / : / : / : / RING/Ubox like zinc-binding domain / RING/Ubox like zinc-binding domain / IBR domain ...: / E3 ubiquitin-protein ligase parkin / RING/Ubox-like zinc-binding domain / Parkin, RING/Ubox like zinc-binding domain / : / : / : / RING/Ubox like zinc-binding domain / RING/Ubox like zinc-binding domain / IBR domain / : / IBR domain / In Between Ring fingers / TRIAD supradomain / TRIAD supradomain profile. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase parkin
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.65 Å
AuthorsTomoo, K.
CitationJournal: Biochim.Biophys.Acta / Year: 2008
Title: Crystal structure and molecular dynamics simulation of ubiquitin-like domain of murine parkin
Authors: Tomoo, K. / Mukai, Y. / In, Y. / Miyagawa, H. / Kitamura, K. / Yamano, A. / Shindo, H. / Ishida, T.
History
DepositionDec 14, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase parkin


Theoretical massNumber of molelcules
Total (without water)8,9181
Polymers8,9181
Non-polymers00
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.06, 46.06, 65.15
Angle α, β, γ (deg.)90, 90, 120
Int Tables number169
Space group name H-MP61

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Components

#1: Protein E3 ubiquitin-protein ligase parkin


Mass: 8918.294 Da / Num. of mol.: 1 / Fragment: Ubiquitin-like domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET28b / Production host: Escherichia coli (E. coli)
References: UniProt: Q9WVS6, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.01 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 4.3
Details: 3M NaCl, 50mM Acetate, pH 4.3, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ DW / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Details: Osmic mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→39.89 Å / Num. obs: 11949 / % possible obs: 99.2 % / Redundancy: 5.38 % / Rmerge(I) obs: 0.019
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 5.17 % / Rmerge(I) obs: 0.077 / % possible all: 98.2

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Processing

Software
NameVersionClassification
CrystalCleardata collection
SOLVEphasing
CNS1.1refinement
CrystalCleardata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.65→39.89 Å / Cross valid method: THROUGHOUT
RfactorNum. reflectionSelection details
Rfree0.244 942 RANDOM
Rwork0.195 --
obs-9420 -
Displacement parametersBiso mean: 19.32 Å2
Refinement stepCycle: LAST / Resolution: 1.65→39.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms626 0 0 44 670
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_angle_deg1.762
X-RAY DIFFRACTIONx_improper_angle_d1.142

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