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Yorodumi- PDB-4zyn: Crystal Structure of Parkin E3 ubiquitin ligase (linker deletion;... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4zyn | ||||||
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Title | Crystal Structure of Parkin E3 ubiquitin ligase (linker deletion; delta 86-130) | ||||||
Components | E3 ubiquitin-protein ligase parkin | ||||||
Keywords | LIGASE / RING domains / Ubiquitin-like domain / RBR | ||||||
Function / homology | Function and homology information Josephin domain DUBs / Aggrephagy / positive regulation of neurotransmitter uptake / regulation protein catabolic process at presynapse / negative regulation of endoplasmic reticulum stress-induced neuron intrinsic apoptotic signaling pathway / cellular response to L-glutamine / PINK1-PRKN Mediated Mitophagy / negative regulation of spontaneous neurotransmitter secretion / negative regulation of intralumenal vesicle formation / Antigen processing: Ubiquitination & Proteasome degradation ...Josephin domain DUBs / Aggrephagy / positive regulation of neurotransmitter uptake / regulation protein catabolic process at presynapse / negative regulation of endoplasmic reticulum stress-induced neuron intrinsic apoptotic signaling pathway / cellular response to L-glutamine / PINK1-PRKN Mediated Mitophagy / negative regulation of spontaneous neurotransmitter secretion / negative regulation of intralumenal vesicle formation / Antigen processing: Ubiquitination & Proteasome degradation / negative regulation of glucokinase activity / negative regulation of exosomal secretion / mitochondrion to lysosome vesicle-mediated transport / response to curcumin / positive regulation of mitochondrial fusion / parkin-mediated stimulation of mitophagy in response to mitochondrial depolarization / cellular response to hydrogen sulfide / Parkin-FBXW7-Cul1 ubiquitin ligase complex / negative regulation of mitochondrial fusion / free ubiquitin chain polymerization / negative regulation of actin filament bundle assembly / positive regulation of mitophagy in response to mitochondrial depolarization / RBR-type E3 ubiquitin transferase / positive regulation of protein linear polyubiquitination / F-box domain binding / negative regulation by host of viral genome replication / mitochondrion localization / positive regulation of autophagy of mitochondrion / positive regulation of mitophagy / mitochondrial fragmentation involved in apoptotic process / cellular response to toxic substance / regulation of dopamine metabolic process / dopaminergic synapse / regulation of cellular response to oxidative stress / negative regulation of excitatory postsynaptic potential / regulation of neurotransmitter secretion / cellular response to L-glutamate / autophagy of mitochondrion / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / protein K6-linked ubiquitination / positive regulation of dendrite extension / norepinephrine metabolic process / positive regulation of proteasomal protein catabolic process / protein localization to mitochondrion / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / negative regulation of JNK cascade / positive regulation of protein localization to membrane / negative regulation of synaptic transmission, glutamatergic / protein K11-linked ubiquitination / protein metabolic process / synaptic transmission, dopaminergic / positive regulation of tumor necrosis factor-mediated signaling pathway / mitochondrial fission / aggresome assembly / ubiquitin conjugating enzyme binding / regulation of mitochondrion organization / aggresome / response to muscle activity / positive regulation of mitochondrial membrane potential / regulation of reactive oxygen species metabolic process / regulation of synaptic vesicle endocytosis / dopamine uptake involved in synaptic transmission / positive regulation of mitochondrial fission / response to corticosterone / dopamine metabolic process / intracellular vesicle / ubiquitin-specific protease binding / positive regulation of ATP biosynthetic process / startle response / negative regulation of release of cytochrome c from mitochondria / regulation of postsynaptic membrane neurotransmitter receptor levels / protein monoubiquitination / positive regulation of insulin secretion involved in cellular response to glucose stimulus / phospholipase binding / cullin family protein binding / protein K63-linked ubiquitination / mitophagy / regulation of protein ubiquitination / response to unfolded protein / negative regulation of mitochondrial fission / negative regulation of insulin secretion / negative regulation of reactive oxygen species metabolic process / positive regulation of DNA binding / cellular response to manganese ion / protein autoubiquitination / protein K48-linked ubiquitination / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of reactive oxygen species biosynthetic process / ubiquitin ligase complex / Hsp70 protein binding / heat shock protein binding / response to endoplasmic reticulum stress / mitochondrion organization / tubulin binding / adult locomotory behavior / proteasomal protein catabolic process / regulation of mitochondrial membrane potential / negative regulation of protein phosphorylation / locomotory behavior / ubiquitin binding Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.54 Å | ||||||
Authors | Lilov, A. / Sauve, V. / Trempe, J.F. / Rodionov, D. / Wang, J. / Gehring, K. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Embo J. / Year: 2015 Title: A Ubl/ubiquitin switch in the activation of Parkin. Authors: Sauve, V. / Lilov, A. / Seirafi, M. / Vranas, M. / Rasool, S. / Kozlov, G. / Sprules, T. / Wang, J. / Trempe, J.F. / Gehring, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zyn.cif.gz | 307.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zyn.ent.gz | 246.8 KB | Display | PDB format |
PDBx/mmJSON format | 4zyn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zy/4zyn ftp://data.pdbj.org/pub/pdb/validation_reports/zy/4zyn | HTTPS FTP |
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-Related structure data
Related structure data | 4k7dS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 47333.859 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: deletion 86-130 / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Park2, Prkn / Plasmid: pGEX-6p1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 References: UniProt: Q9JK66, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.14 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.3M Ammonium Sulfate, 0.1M HEPES pH 7.5, 18% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Nov 28, 2012 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Rigaku VariMax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.54→50 Å / Num. obs: 28338 / % possible obs: 95 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.047 / Rrim(I) all: 0.131 / Χ2: 1.108 / Net I/av σ(I): 12.158 / Net I/σ(I): 6.2 / Num. measured all: 230168 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4K7D Resolution: 2.54→36.62 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.918 / WRfactor Rfree: 0.2326 / WRfactor Rwork: 0.1874 / FOM work R set: 0.9021 / SU B: 7.373 / SU ML: 0.095 / SU R Cruickshank DPI: 0.1172 / SU Rfree: 0.0589 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.117 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 235.59 Å2 / Biso mean: 66.684 Å2 / Biso min: 5.54 Å2
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Refinement step | Cycle: final / Resolution: 2.54→36.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.541→2.607 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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