+Open data
-Basic information
Entry | Database: PDB / ID: 2zeq | ||||||
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Title | Crystal structure of ubiquitin-like domain of murine Parkin | ||||||
Components | E3 ubiquitin-protein ligase parkin | ||||||
Keywords | LIGASE / Parkin / ubiquitin-like domain / Alternative splicing / Cell junction / Cell projection / Cytoplasm / Endoplasmic reticulum / Membrane / Metal-binding / Nucleus / Postsynaptic cell membrane / S-nitrosylation / Synapse / Ubl conjugation / Ubl conjugation pathway / Zinc / Zinc-finger | ||||||
Function / homology | Function and homology information positive regulation of neurotransmitter uptake / regulation protein catabolic process at presynapse / negative regulation of endoplasmic reticulum stress-induced neuron intrinsic apoptotic signaling pathway / mitochondrion-derived vesicle / negative regulation of spontaneous neurotransmitter secretion / negative regulation of intralumenal vesicle formation / PINK1-PRKN Mediated Mitophagy / negative regulation of exosomal secretion / Josephin domain DUBs / mitochondrion to lysosome vesicle-mediated transport ...positive regulation of neurotransmitter uptake / regulation protein catabolic process at presynapse / negative regulation of endoplasmic reticulum stress-induced neuron intrinsic apoptotic signaling pathway / mitochondrion-derived vesicle / negative regulation of spontaneous neurotransmitter secretion / negative regulation of intralumenal vesicle formation / PINK1-PRKN Mediated Mitophagy / negative regulation of exosomal secretion / Josephin domain DUBs / mitochondrion to lysosome vesicle-mediated transport / positive regulation of mitochondrial fusion / Regulation of necroptotic cell death / parkin-mediated stimulation of mitophagy in response to mitochondrial depolarization / cellular response to hydrogen sulfide / Aggrephagy / 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 / cellular response to L-glutamate / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / protein K6-linked ubiquitination / Antigen processing: Ubiquitination & Proteasome degradation / autophagy of mitochondrion / 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 / protein metabolic process / negative regulation of JNK cascade / protein K11-linked ubiquitination / positive regulation of tumor necrosis factor-mediated signaling pathway / synaptic transmission, dopaminergic / mitochondrial fission / aggresome assembly / ubiquitin conjugating enzyme binding / regulation of mitochondrion organization / aggresome / positive regulation of mitochondrial membrane potential / 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 / 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 / negative regulation of insulin secretion / negative regulation of reactive oxygen species metabolic process / protein K48-linked ubiquitination / 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 / synaptic transmission, glutamatergic / regulation of autophagy / G protein-coupled receptor binding / PDZ domain binding / proteasomal protein catabolic process / protein catabolic process Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SAD / Resolution: 1.65 Å | ||||||
Authors | Tomoo, K. | ||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2008 Title: Crystal structure and molecular dynamics simulation of ubiquitin-like domain of murine parkin Authors: Tomoo, K. / Mukai, Y. / In, Y. / Miyagawa, H. / Kitamura, K. / Yamano, A. / Shindo, H. / Ishida, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zeq.cif.gz | 27.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zeq.ent.gz | 18.2 KB | Display | PDB format |
PDBx/mmJSON format | 2zeq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ze/2zeq ftp://data.pdbj.org/pub/pdb/validation_reports/ze/2zeq | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 8918.294 Da / Num. of mol.: 1 / Fragment: Ubiquitin-like domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET28b / Production host: Escherichia coli (E. coli) References: UniProt: Q9WVS6, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.24 Å3/Da / Density % sol: 45.01 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 4.3 Details: 3M NaCl, 50mM Acetate, pH 4.3, VAPOR DIFFUSION, HANGING DROP, temperature 288K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ DW / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Details: Osmic mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→39.89 Å / Num. obs: 11949 / % possible obs: 99.2 % / Redundancy: 5.38 % / Rmerge(I) obs: 0.019 |
Reflection shell | Resolution: 1.65→1.71 Å / Redundancy: 5.17 % / Rmerge(I) obs: 0.077 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.65→39.89 Å / Cross valid method: THROUGHOUT
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Displacement parameters | Biso mean: 19.32 Å2 | ||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→39.89 Å
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Refine LS restraints |
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