+Open data
-Basic information
Entry | Database: PDB / ID: 5c9v | |||||||||
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Title | Structure of human Parkin G319A | |||||||||
Components | E3 ubiquitin-protein ligase parkin | |||||||||
Keywords | SIGNALING PROTEIN / Parkin / ubiquitin / E3 ligase / RBR / Parkinson's disease / mitophagy / cell signalling | |||||||||
Function / homology | Function and homology information 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 / negative regulation of primary amine oxidase activity / negative regulation of spontaneous neurotransmitter secretion / negative regulation of intralumenal vesicle formation / regulation of protein targeting to mitochondrion / negative regulation of glucokinase 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 / negative regulation of primary amine oxidase activity / negative regulation of spontaneous neurotransmitter secretion / negative regulation of intralumenal vesicle formation / regulation of protein targeting to mitochondrion / negative regulation of glucokinase activity / mitochondrion to lysosome vesicle-mediated transport / negative regulation of exosomal secretion / positive regulation of mitochondrial fusion / parkin-mediated stimulation of mitophagy in response to mitochondrial depolarization / protein K29-linked ubiquitination / Lewy body / protein K27-linked ubiquitination / Parkin-FBXW7-Cul1 ubiquitin ligase complex / free ubiquitin chain polymerization / negative regulation of actin filament bundle assembly / regulation of synaptic vesicle transport / negative regulation of mitochondrial fusion / RBR-type E3 ubiquitin transferase / positive regulation of mitophagy in response to mitochondrial depolarization / positive regulation of protein linear polyubiquitination / F-box domain binding / negative regulation by host of viral genome replication / positive regulation of mitophagy / dopaminergic synapse / cellular response to toxic substance / regulation of dopamine metabolic process / regulation of necroptotic process / regulation of cellular response to oxidative stress / 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 / positive regulation of protein localization to membrane / negative regulation of JNK cascade / protein K11-linked ubiquitination / positive regulation of tumor necrosis factor-mediated signaling pathway / cellular response to dopamine / autophagy of mitochondrion / mitochondrial fission / aggresome assembly / ubiquitin conjugating enzyme binding / regulation of canonical Wnt signaling pathway / ERAD pathway / aggresome / regulation of mitochondrion organization / regulation of reactive oxygen species metabolic process / dopamine uptake involved in synaptic transmission / regulation of synaptic vesicle endocytosis / positive regulation of mitochondrial fission / dopamine metabolic process / regulation of dopamine secretion / ubiquitin-specific protease binding / protein monoubiquitination / startle response / negative regulation of release of cytochrome c from mitochondria / protein K63-linked ubiquitination / cullin family protein binding / phospholipase binding / mitophagy / regulation of protein ubiquitination / regulation of glucose metabolic process / negative regulation of insulin secretion / protein K48-linked ubiquitination / negative regulation of reactive oxygen species metabolic process / protein autoubiquitination / positive regulation of DNA binding / cellular response to unfolded protein / cellular response to manganese ion / ubiquitin ligase complex / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / Hsp70 protein binding / heat shock protein binding / mitochondrion organization / PINK1-PRKN Mediated Mitophagy / response to endoplasmic reticulum stress / tubulin binding / adult locomotory behavior / Josephin domain DUBs / regulation of mitochondrial membrane potential / negative regulation of protein phosphorylation / ubiquitin binding / learning / synaptic transmission, glutamatergic / central nervous system development / regulation of autophagy / G protein-coupled receptor binding / PDZ domain binding / proteasomal protein catabolic process / macroautophagy / negative regulation of canonical Wnt signaling pathway / protein destabilization / regulation of protein stability Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | |||||||||
Authors | Wauer, T. / Komander, D. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Nature / Year: 2015 Title: Mechanism of phospho-ubiquitin-induced PARKIN activation. Authors: Wauer, T. / Simicek, M. / Schubert, A. / Komander, D. #1: Journal: EMBO J. / Year: 2013 Title: Structure of the human Parkin ligase domain in an autoinhibited state. Authors: Wauer, T. / Komander, D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5c9v.cif.gz | 138.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5c9v.ent.gz | 107 KB | Display | PDB format |
PDBx/mmJSON format | 5c9v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c9/5c9v ftp://data.pdbj.org/pub/pdb/validation_reports/c9/5c9v | HTTPS FTP |
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-Related structure data
Related structure data | 5cawC 4bm9S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-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: 36892.129 Da / Num. of mol.: 1 / Fragment: UNP residues 137-465 / Mutation: G319A Source method: isolated from a genetically manipulated source Details: engineered mutation at position G319A / Source: (gene. exp.) Homo sapiens (human) / Gene: PARK2, PRKN / Plasmid: pOPINK Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: O60260, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) | ||||||
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#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.63 Å3/Da / Density % sol: 66.1 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 1.8 M lithium sulphate, 0.01 M MgCl2, 0.05 M MES pH 5.6 PH range: 5.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 20, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9173 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→86.68 Å / Num. obs: 22270 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Biso Wilson estimate: 42.5 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 2.35→2.43 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.1 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4bm9 Resolution: 2.35→84.68 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.8 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 54.3 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.35→84.68 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 7.8845 Å / Origin y: 31.4194 Å / Origin z: 36.9402 Å
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Refinement TLS group | Selection details: chain A |