+Open data
-Basic information
Entry | Database: PDB / ID: 4k7d | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Parkin C-terminal RING domains | ||||||
Components | E3 ubiquitin-protein ligase parkin | ||||||
Keywords | LIGASE / RING domains / zinc fingers / RBR ubiquitin ligase / E3 ubiquitin protein ligase / Ubiquitin / UbcH7 | ||||||
Function / homology | Function and homology information Josephin domain DUBs / 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 / negative regulation of intralumenal vesicle formation / Antigen processing: Ubiquitination & Proteasome degradation ...Josephin domain DUBs / 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 / negative regulation of intralumenal vesicle formation / Antigen processing: Ubiquitination & Proteasome degradation / negative regulation of glucokinase activity / negative regulation of exosomal secretion / mitochondrion to lysosome vesicle-mediated transport / 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 / free ubiquitin chain polymerization / negative regulation of actin filament bundle assembly / 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 / mitochondrion localization / dopaminergic synapse / positive regulation of autophagy of mitochondrion / mitochondrial fragmentation involved in apoptotic process / positive regulation of mitophagy / cellular response to toxic substance / regulation of dopamine metabolic process / regulation of cellular response to oxidative stress / negative regulation of excitatory postsynaptic potential / regulation of neurotransmitter secretion / autophagy of mitochondrion / cellular response to L-glutamate / 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 synaptic transmission, glutamatergic / 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 / protein metabolic process / synaptic transmission, dopaminergic / 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 / dopamine uptake involved in synaptic transmission / regulation of synaptic vesicle endocytosis / positive regulation of mitochondrial fission / dopamine metabolic process / response to corticosterone / intracellular vesicle / ubiquitin-specific protease binding / positive regulation of ATP biosynthetic process / startle response / negative regulation of release of cytochrome c from mitochondria / protein monoubiquitination / positive regulation of insulin secretion involved in cellular response to glucose stimulus / protein K63-linked ubiquitination / regulation of postsynaptic membrane neurotransmitter receptor levels / cullin family protein binding / phospholipase binding / mitophagy / regulation of protein ubiquitination / negative regulation of mitochondrial fission / response to unfolded protein / 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 manganese ion / protein autoubiquitination / ubiquitin ligase complex / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / negative regulation of reactive oxygen species biosynthetic process / Hsp70 protein binding / heat shock protein binding / response to endoplasmic reticulum stress / mitochondrion organization / tubulin binding / adult locomotory behavior / locomotory behavior / regulation of mitochondrial membrane potential / negative regulation of protein phosphorylation / ubiquitin binding / learning Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å | ||||||
Authors | Sauve, V. / Trempe, J.-F. / Menade, M. / Gehring, K. | ||||||
Citation | Journal: Science / Year: 2013 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4k7d.cif.gz | 195.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4k7d.ent.gz | 155 KB | Display | PDB format |
PDBx/mmJSON format | 4k7d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k7/4k7d ftp://data.pdbj.org/pub/pdb/validation_reports/k7/4k7d | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 36831.070 Da / Num. of mol.: 3 / Fragment: C-terminal RING domains (141-465) Source method: isolated from a genetically manipulated source Details: Codon-optimized for E.coli expression / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Park2, Prkn / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q9JK66, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) #2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | ChemComp-CL / | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.15 Å3/Da / Density % sol: 60.97 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.9 M sodium malonate pH 7.0, 0.1 M HEPES pH 7.0, 5% (v/v) glycerol, 56 mM 2-mercaptoethanol, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.2824 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 16, 2012 / Details: Vertical focusing mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: ACCEL/BRUKER DCM, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.2824 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.8→53.33 Å / Num. all: 35155 / Num. obs: 35121 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 9.7 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 19.9 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Phasing
Phasing | Method: SAD |
---|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 2.8→53.31 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8301 / SU ML: 0.32 / σ(F): 1.36 / Phase error: 23.44 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 126.57 Å2 / Biso mean: 53.4322 Å2 / Biso min: 22.23 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.337 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→53.31 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13
|