+Open data
-Basic information
Entry | Database: PDB / ID: 6hue | ||||||
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Title | ParkinS65N | ||||||
Components | E3 ubiquitin-protein ligase parkin | ||||||
Keywords | LIGASE / E3 ligase | ||||||
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 / negative regulation of exosomal secretion / mitochondrion to lysosome vesicle-mediated transport / 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 / dopaminergic synapse / positive regulation of mitophagy / cellular response to toxic substance / regulation of dopamine metabolic process / regulation of necroptotic process / regulation of cellular response to oxidative stress / 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 / 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 / mitochondrial fission / aggresome assembly / ubiquitin conjugating enzyme binding / regulation of canonical Wnt signaling pathway / regulation of mitochondrion organization / aggresome / ERAD pathway / 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 / startle response / negative regulation of release of cytochrome c from mitochondria / protein monoubiquitination / 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 / negative regulation of reactive oxygen species metabolic process / protein K48-linked ubiquitination / positive regulation of DNA binding / cellular response to unfolded protein / cellular response to manganese ion / protein autoubiquitination / ubiquitin ligase complex / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / Hsp70 protein binding / heat shock protein binding / PINK1-PRKN Mediated Mitophagy / response to endoplasmic reticulum stress / mitochondrion organization / 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: 2.85 Å | ||||||
Authors | McWilliams, T.G. / Barini, E. / Pohjolan-Pirhonen, R. / Brooks, S.P. / Singh, F. / Burel, S. / Balk, K. / Kumar, A. / Montava-Garriga, L. / Prescott, A.R. ...McWilliams, T.G. / Barini, E. / Pohjolan-Pirhonen, R. / Brooks, S.P. / Singh, F. / Burel, S. / Balk, K. / Kumar, A. / Montava-Garriga, L. / Prescott, A.R. / Hassoun, S.M. / Mouton-Liger, F. / Ball, G. / Hills, R. / Knebel, A. / Ulusoy, A. / Di Monte, D.A. / Tamjar, J. / Antico, O. / Fears, K. / Smith, L. / Brambilla, R. / Palin, E. / Valori, M. / Eerola-Rautio, J. / Tienari, P. / Corti, O. / Dunnett, S.B. / Ganley, I.G. / Suomalainen, A. / Muqit, M.M.K. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Open Biology / Year: 2018 Title: Phosphorylation of Parkin at serine 65 is essential for its activation in vivo . Authors: McWilliams, T.G. / Barini, E. / Pohjolan-Pirhonen, R. / Brooks, S.P. / Singh, F. / Burel, S. / Balk, K. / Kumar, A. / Montava-Garriga, L. / Prescott, A.R. / Hassoun, S.M. / Mouton-Liger, F. ...Authors: McWilliams, T.G. / Barini, E. / Pohjolan-Pirhonen, R. / Brooks, S.P. / Singh, F. / Burel, S. / Balk, K. / Kumar, A. / Montava-Garriga, L. / Prescott, A.R. / Hassoun, S.M. / Mouton-Liger, F. / Ball, G. / Hills, R. / Knebel, A. / Ulusoy, A. / Di Monte, D.A. / Tamjar, J. / Antico, O. / Fears, K. / Smith, L. / Brambilla, R. / Palin, E. / Valori, M. / Eerola-Rautio, J. / Tienari, P. / Corti, O. / Dunnett, S.B. / Ganley, I.G. / Suomalainen, A. / Muqit, M.M.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hue.cif.gz | 175.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hue.ent.gz | 136.1 KB | Display | PDB format |
PDBx/mmJSON format | 6hue.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hu/6hue ftp://data.pdbj.org/pub/pdb/validation_reports/hu/6hue | HTTPS FTP |
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-Related structure data
Related structure data | 5c1zS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 45652.039 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PRKN, PARK2 / Production host: Escherichia coli (E. coli) References: UniProt: O60260, RBR-type E3 ubiquitin transferase |
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-Non-polymers , 5 types, 181 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | ChemComp-GOL / #5: Chemical | #6: 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: 2.51 Å3/Da / Density % sol: 51.07 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 100mM BIS-TRIS pH 5.5, 200mM LiSO4 and 20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 17, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.966 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→47.98 Å / Num. obs: 21291 / % possible obs: 96.1 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.125 / Net I/σ(I): 4.5 |
Reflection shell | Resolution: 2.85→2.95 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5C1Z Resolution: 2.85→47.98 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.913 / SU B: 24.598 / SU ML: 0.407 / Cross valid method: THROUGHOUT / ESU R Free: 0.422 / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 64.964 Å2
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Refinement step | Cycle: 1 / Resolution: 2.85→47.98 Å
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Refine LS restraints |
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