+Open data
-Basic information
Entry | Database: PDB / ID: 8wzo | ||||||
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Title | Parkin in complex with phospho NEDD8 | ||||||
Components |
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Keywords | LIGASE / E3 Ligase | ||||||
Function / homology | Function and homology information negative regulation of primary amine oxidase activity / positive regulation of retrograde transport, endosome to Golgi / regulation of lipid transport / positive regulation of neurotransmitter uptake / regulation protein catabolic process at presynapse / negative regulation of endoplasmic reticulum stress-induced neuron intrinsic apoptotic signaling pathway / regulation of protein targeting to mitochondrion / negative regulation of spontaneous neurotransmitter secretion / negative regulation of intralumenal vesicle formation / negative regulation of glucokinase activity ...negative regulation of primary amine oxidase activity / positive regulation of retrograde transport, endosome to Golgi / regulation of lipid transport / positive regulation of neurotransmitter uptake / regulation protein catabolic process at presynapse / negative regulation of endoplasmic reticulum stress-induced neuron intrinsic apoptotic signaling pathway / regulation of protein targeting to mitochondrion / negative regulation of spontaneous neurotransmitter secretion / negative regulation of intralumenal vesicle formation / negative regulation of glucokinase activity / negative regulation of exosomal secretion / mitochondrion to lysosome vesicle-mediated transport / type 2 mitophagy / Lewy body / protein K27-linked ubiquitination / Parkin-FBXW7-Cul1 ubiquitin ligase complex / negative regulation of actin filament bundle assembly / positive regulation of mitochondrial fusion / free ubiquitin chain polymerization / protein K29-linked ubiquitination / regulation of synaptic vesicle transport / negative regulation of mitochondrial fusion / : / positive regulation of protein linear polyubiquitination / F-box domain binding / RBR-type E3 ubiquitin transferase / negative regulation by host of viral genome replication / cellular response to toxic substance / positive regulation of mitophagy / regulation of necroptotic process / regulation of cellular response to oxidative stress / regulation of dopamine metabolic process / 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 proteasomal protein catabolic process / norepinephrine metabolic process / protein localization to mitochondrion / positive regulation of protein localization to membrane / negative regulation of JNK cascade / regulation of proteolysis / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / positive regulation of tumor necrosis factor-mediated signaling pathway / cellular response to dopamine / mitochondrial fission / protein K11-linked ubiquitination / protein neddylation / ubiquitin conjugating enzyme binding / aggresome assembly / autophagy of mitochondrion / regulation of mitochondrion organization / regulation of canonical Wnt signaling pathway / aggresome / regulation of reactive oxygen species metabolic process / regulation of synaptic vesicle endocytosis / positive regulation of DNA binding / protein deubiquitination / positive regulation of mitochondrial fission / dopamine uptake involved in synaptic transmission / ubiquitin-specific protease binding / regulation of dopamine secretion / dopamine metabolic process / negative regulation of release of cytochrome c from mitochondria / startle response / TGF-beta receptor signaling activates SMADs / protein monoubiquitination / cullin family protein binding / phospholipase binding / protein K63-linked ubiquitination / regulation of protein ubiquitination / regulation of glucose metabolic process / mitophagy / negative regulation of reactive oxygen species metabolic process / anatomical structure morphogenesis / cellular response to unfolded protein / cellular response to manganese ion / protein autoubiquitination / proteasomal protein catabolic process / negative regulation of insulin secretion / protein K48-linked ubiquitination / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / ERAD pathway / ubiquitin ligase complex / heat shock protein binding / Hsp70 protein binding / response to endoplasmic reticulum stress / tubulin binding / adult locomotory behavior / PINK1-PRKN Mediated Mitophagy / Josephin domain DUBs / negative regulation of protein phosphorylation / regulation of mitochondrial membrane potential / ubiquitin binding / learning / mitochondrion organization / regulation of autophagy / central nervous system development / synaptic transmission, glutamatergic / G protein-coupled receptor binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Lenka, D.R. / Kumar, A. | ||||||
Funding support | India, 1items
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Citation | Journal: Structure Title: Parkin in complex with phospho NEDD8 Authors: Lenka, D.R. / Kumar, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8wzo.cif.gz | 97.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8wzo.ent.gz | 68.9 KB | Display | PDB format |
PDBx/mmJSON format | 8wzo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8wzo_validation.pdf.gz | 454.1 KB | Display | wwPDB validaton report |
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Full document | 8wzo_full_validation.pdf.gz | 457.6 KB | Display | |
Data in XML | 8wzo_validation.xml.gz | 20 KB | Display | |
Data in CIF | 8wzo_validation.cif.gz | 26.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wz/8wzo ftp://data.pdbj.org/pub/pdb/validation_reports/wz/8wzo | HTTPS FTP |
-Related structure data
Related structure data | 8wznC 5n2wS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 36438.613 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PRKN / Production host: Escherichia coli (E. coli) / References: UniProt: O60260 | ||||||
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#2: Protein | Mass: 8741.034 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NEDD8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15843 | ||||||
#3: Chemical | ChemComp-ZN / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.57 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion Details: 0.02 M Sodium/potassium phosphate, 0.1 M Bis-Tris propane, 7.5, 20% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.8731 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 28, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8731 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→44.52 Å / Num. obs: 21772 / % possible obs: 99.8 % / Redundancy: 4.3 % / CC1/2: 0.993 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 2.25→2.32 Å / Num. unique obs: 1974 / CC1/2: 0.643 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5N2W Resolution: 2.25→40.947 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.923 / WRfactor Rfree: 0.242 / WRfactor Rwork: 0.201 / SU B: 7.117 / SU ML: 0.173 / Average fsc free: 0.8838 / Average fsc work: 0.9042 / Cross valid method: FREE R-VALUE / ESU R: 0.294 / ESU R Free: 0.221 Details: Hydrogens have been added in their riding positions
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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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.106 Å2
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Refinement step | Cycle: LAST / Resolution: 2.25→40.947 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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