+Open data
-Basic information
Entry | Database: PDB / ID: 6glc | |||||||||||||||
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Title | Structure of phospho-Parkin bound to phospho-ubiquitin | |||||||||||||||
Components |
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Keywords | LIGASE / ubiquitin / Parkin / phospho-ubiquitin / Parkinson's disease / E3 ligase / RBR domain / mitophagy | |||||||||||||||
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 / negative regulation of spontaneous neurotransmitter secretion / regulation of protein targeting to mitochondrion / 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 / negative regulation of spontaneous neurotransmitter secretion / regulation of protein targeting to mitochondrion / negative regulation of intralumenal vesicle formation / 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 / regulation of synaptic vesicle transport / 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 / positive regulation of mitophagy / cellular response to toxic substance / regulation of dopamine metabolic process / regulation of necroptotic process / dopaminergic synapse / 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 / negative regulation of JNK cascade / positive regulation of protein localization to membrane / protein K11-linked ubiquitination / cellular response to dopamine / positive regulation of tumor necrosis factor-mediated signaling pathway / mitochondrial fission / aggresome assembly / ubiquitin conjugating enzyme binding / regulation of canonical Wnt signaling pathway / regulation of mitochondrion organization / hypothalamus gonadotrophin-releasing hormone neuron development / aggresome / female meiosis I / regulation of reactive oxygen species metabolic process / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / fat pad development / regulation of synaptic vesicle endocytosis / dopamine uptake involved in synaptic transmission / positive regulation of mitochondrial fission / dopamine metabolic process / female gonad development / regulation of dopamine secretion / ubiquitin-specific protease binding / seminiferous tubule development / startle response / male meiosis I / negative regulation of release of cytochrome c from mitochondria / ERAD pathway / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / protein monoubiquitination / phospholipase binding / cullin family protein binding / protein K63-linked ubiquitination / mitophagy / regulation of protein ubiquitination / regulation of glucose metabolic process / negative regulation of insulin secretion / negative regulation of reactive oxygen species metabolic process / cellular response to unfolded protein / 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 / energy homeostasis / regulation of neuron apoptotic process / regulation of proteasomal protein catabolic process / ubiquitin ligase complex / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||||||||
Authors | Gladkova, C. / Maslen, S.L. / Skehel, J.M. / Komander, D. | |||||||||||||||
Funding support | United Kingdom, 4items
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Citation | Journal: Nature / Year: 2018 Title: Mechanism of parkin activation by PINK1. Authors: Gladkova, C. / Maslen, S.L. / Skehel, J.M. / Komander, D. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6glc.cif.gz | 181.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6glc.ent.gz | 140.9 KB | Display | PDB format |
PDBx/mmJSON format | 6glc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gl/6glc ftp://data.pdbj.org/pub/pdb/validation_reports/gl/6glc | HTTPS FTP |
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-Related 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
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 43008.551 Da / Num. of mol.: 1 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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#2: Protein | Mass: 8640.854 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47 |
-Non-polymers , 5 types, 176 molecules
#3: Chemical | ChemComp-ZN / #4: Chemical | #5: Chemical | ChemComp-MPD / ( | #6: Chemical | ChemComp-SO4 / | #7: 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: 2.32 Å3/Da / Density % sol: 40.56 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 12.5% (w/v) PEG 1000, 12.5% (w/v) PEG 3350, 12.5% (v/v) MPD, 0.03 M of each sodium nitrate, disodium hydrogen phosphate, ammonium sulphate, 0.1 M MOPS/HEPES-Na (pH 7.5) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96859 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 22, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96859 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→72.69 Å / Num. obs: 40324 / % possible obs: 100 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 1.8→1.84 Å / Rmerge(I) obs: 0.773 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2339 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5n2w, 5c1z Resolution: 1.8→59.786 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.46 / Phase error: 22.14
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→59.786 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: -6.6329 Å / Origin y: -26.8647 Å / Origin z: -16.2338 Å
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Refinement TLS group | Selection details: all |