+Open data
-Basic information
Entry | Database: PDB / ID: 5c1z | ||||||
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Title | Parkin (UblR0RBR) | ||||||
Components | E3 ubiquitin-protein ligase parkin | ||||||
Keywords | 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 / mitochondrion to lysosome vesicle-mediated transport / negative regulation of exosomal secretion / 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 / norepinephrine metabolic process / cellular response to toxic substance / dopaminergic synapse / regulation of dopamine metabolic process / regulation of necroptotic process / regulation of cellular response to oxidative stress / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / protein K6-linked ubiquitination / positive regulation of autophagy of mitochondrion / positive regulation of dendrite extension / 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 / cellular response to dopamine / positive regulation of tumor necrosis factor-mediated signaling pathway / ERAD pathway / mitochondrial fission / aggresome assembly / ubiquitin conjugating enzyme binding / regulation of canonical Wnt signaling pathway / aggresome / regulation of mitochondrion organization / dopamine uptake involved in synaptic transmission / regulation of reactive oxygen species metabolic process / regulation of synaptic vesicle endocytosis / startle response / positive regulation of mitochondrial fission / autophagy of mitochondrion / dopamine metabolic process / regulation of dopamine secretion / protein monoubiquitination / ubiquitin-specific protease binding / mitophagy / negative regulation of release of cytochrome c from mitochondria / cullin family protein binding / protein K63-linked ubiquitination / phospholipase binding / regulation of protein ubiquitination / regulation of glucose metabolic process / protein K48-linked ubiquitination / negative regulation of insulin secretion / negative regulation of reactive oxygen species metabolic process / 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 / mitochondrion organization / heat shock protein binding / response to endoplasmic reticulum stress / PINK1-PRKN Mediated Mitophagy / adult locomotory behavior / tubulin binding / Josephin domain DUBs / Hsp70 protein binding / regulation of mitochondrial membrane potential / negative regulation of protein phosphorylation / learning / ubiquitin binding / central nervous system development / synaptic transmission, glutamatergic / 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: 1.79 Å | ||||||
Authors | kumar, A. / Aguirre, J.D. / Condos, T.E.C. / Martinez-Torres, R.J. / Chaugule, V.K. / Toth, R. / Sundaramoorthy, R. / Mercier, P. / Knebel, A. / Spratt, D.E. ...kumar, A. / Aguirre, J.D. / Condos, T.E.C. / Martinez-Torres, R.J. / Chaugule, V.K. / Toth, R. / Sundaramoorthy, R. / Mercier, P. / Knebel, A. / Spratt, D.E. / Barber, K.R. / Shaw, G.S. / Walden, H. | ||||||
Citation | Journal: Embo J. / Year: 2015 Title: Disruption of the autoinhibited state primes the E3 ligase parkin for activation and catalysis. Authors: Kumar, A. / Aguirre, J.D. / Condos, T.E. / Martinez-Torres, R.J. / Chaugule, V.K. / Toth, R. / Sundaramoorthy, R. / Mercier, P. / Knebel, A. / Spratt, D.E. / Barber, K.R. / Shaw, G.S. / Walden, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5c1z.cif.gz | 342.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5c1z.ent.gz | 276.3 KB | Display | PDB format |
PDBx/mmJSON format | 5c1z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c1/5c1z ftp://data.pdbj.org/pub/pdb/validation_reports/c1/5c1z | HTTPS FTP |
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-Related structure data
Related structure data | 5c23C 4k95S S: Starting model for refinement C: citing same article (ref.) |
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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: 45625.012 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PARK2, PRKN / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: O60260, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) |
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-Non-polymers , 5 types, 735 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 |
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-Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.9 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / pH: 5.5 / Details: LiSO4, PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9174 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 23, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9174 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→56.36 Å / Num. all: 87826 / Num. obs: 87891 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 32.3 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 1.79→1.85 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 1.8 / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4K95 Resolution: 1.79→56.36 Å / Cor.coef. Fo:Fc: 0.9505 / Cor.coef. Fo:Fc free: 0.9461 / SU R Cruickshank DPI: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.124 / SU Rfree Blow DPI: 0.111 / SU Rfree Cruickshank DPI: 0.107
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Displacement parameters | Biso mean: 49.13 Å2
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Refine analyze | Luzzati coordinate error obs: 0.255 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.79→56.36 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.79→1.84 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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