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Open data
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Basic information
Entry | Database: PDB / ID: 4k95 | ||||||
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Title | Crystal Structure of Parkin | ||||||
![]() | E3 ubiquitin-protein ligase parkin | ||||||
![]() | LIGASE / Ubiquitin-like domain / RING domains / zinc fingers / RBR ubiquitin ligase / zinc finger / UbcH7 / ubiquitin / mitochondria | ||||||
Function / homology | ![]() Josephin domain DUBs / Regulation of necroptotic cell death / 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 / Antigen processing: Ubiquitination & Proteasome degradation ...Josephin domain DUBs / Regulation of necroptotic cell death / 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 / Antigen processing: Ubiquitination & Proteasome degradation / negative regulation of intralumenal vesicle formation / negative regulation of glucokinase activity / mitochondrion to lysosome vesicle-mediated transport / negative regulation of exosomal secretion / 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 mitophagy / cellular response to toxic substance / mitochondrial fragmentation involved in apoptotic process / regulation of cellular response to oxidative stress / regulation of dopamine metabolic process / dopaminergic synapse / 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 / positive regulation of dendrite extension / protein K6-linked ubiquitination / norepinephrine metabolic process / positive regulation of proteasomal protein catabolic process / protein localization to mitochondrion / 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 / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / 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 / positive regulation of mitochondrial membrane potential / response to muscle activity / 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 / intracellular vesicle / dopamine metabolic process / positive regulation of ATP biosynthetic process / ubiquitin-specific protease binding / 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 / cullin family protein binding / phospholipase binding / protein K63-linked ubiquitination / mitophagy / regulation of protein ubiquitination / response to unfolded protein / negative regulation of mitochondrial fission / negative regulation of reactive oxygen species metabolic process / proteasomal protein catabolic process / cellular response to manganese ion / positive regulation of DNA binding / negative regulation of insulin secretion / 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 / heat shock protein binding / Hsp70 protein binding / response to endoplasmic reticulum stress / tubulin binding / mitochondrion organization / adult locomotory behavior / negative regulation of protein phosphorylation / regulation of mitochondrial membrane potential / learning / ubiquitin binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Seirafi, M. / Menade, M. / Sauve, V. / Kozlov, G. / Trempe, J.-F. / Nagar, B. / Gehring, K. | ||||||
![]() | ![]() Title: Structure of parkin reveals mechanisms for ubiquitin ligase activation. Authors: Trempe, J.F. / Sauve, V. / Grenier, K. / Seirafi, M. / Tang, M.Y. / Menade, M. / Al-Abdul-Wahid, S. / Krett, J. / Wong, K. / Kozlov, G. / Nagar, B. / Fon, E.A. / Gehring, K. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 778.1 KB | Display | ![]() |
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PDB format | ![]() | 621.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 507.8 KB | Display | ![]() |
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Full document | ![]() | 661.8 KB | Display | |
Data in XML | ![]() | 112.2 KB | Display | |
Data in CIF | ![]() | 160.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4k7dSC ![]() 2zeqS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
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Components
#1: Protein | Mass: 52155.113 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Details: Codon-optimized for E.coli expression / Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q9JK66, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) #2: Chemical | ChemComp-ZN / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.91 Å3/Da / Density % sol: 57.74 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 22.5% PEG3350, 0.2 M (NH4)2SO4, 0.1 M HEPES pH 7.0, 10% (v/v) glycerol, 3% sorbitol and 25 mM 2-mercaptoethanol, vapor diffusion, hanging drop, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 11, 2012 / Details: mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9183 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 6.5→50 Å / Num. all: 14952 / Num. obs: 14922 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.2 % / Biso Wilson estimate: 227 Å2 / Rmerge(I) obs: 0.172 / Χ2: 1.574 / Net I/σ(I): 15.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entries: 4K7D (rat parkin 141-465) and 2ZEQ (mouse parkin 1-72) Resolution: 6.499→49.334 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7121 / SU ML: 1.11 / σ(F): 1.34 / Phase error: 34.11 / 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 max: 213.59 Å2 / Biso mean: 88.6785 Å2 / Biso min: 28.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 6.499→49.334 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: 5
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