+Open data
-Basic information
Entry | Database: PDB / ID: 5n38 | |||||||||
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Title | S65DParkin and pUB complex | |||||||||
Components |
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Keywords | LIGASE / S65DParkin pUB complex / splicing | |||||||||
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 / 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 / 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 necroptotic process / regulation of cellular response to oxidative stress / regulation of dopamine metabolic process / dopaminergic synapse / 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 / protein K11-linked ubiquitination / negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway / cellular response to dopamine / positive regulation of tumor necrosis factor-mediated signaling pathway / mitochondrial fission / aggresome assembly / ubiquitin conjugating enzyme binding / regulation of mitochondrion organization / hypothalamus gonadotrophin-releasing hormone neuron development / regulation of canonical Wnt signaling pathway / aggresome / female meiosis I / positive regulation of protein monoubiquitination / regulation of reactive oxygen species metabolic process / regulation of synaptic vesicle endocytosis / mitochondrion transport along microtubule / fat pad development / dopamine uptake involved in synaptic transmission / positive regulation of mitochondrial fission / dopamine metabolic process / female gonad development / seminiferous tubule development / regulation of dopamine secretion / ubiquitin-specific protease binding / startle response / male meiosis I / negative regulation of release of cytochrome c from mitochondria / protein monoubiquitination / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / cullin family protein binding / phospholipase binding / protein K63-linked ubiquitination / mitophagy / regulation of protein ubiquitination / regulation of glucose metabolic process / negative regulation of reactive oxygen species metabolic process / cellular response to unfolded protein / 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 / energy homeostasis / regulation of neuron apoptotic process / regulation of proteasomal protein catabolic process / ERAD pathway / 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 Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | |||||||||
Authors | Kumar, A. / Chaugule, V.K. / Johnson, C. / Toth, R. / Sundaramoorthy, R. / Knebel, A. / Walden, H. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Nat. Struct. Mol. Biol. / Year: 2017 Title: Parkin-phosphoubiquitin complex reveals cryptic ubiquitin-binding site required for RBR ligase activity. Authors: Kumar, A. / Chaugule, V.K. / Condos, T.E.C. / Barber, K.R. / Johnson, C. / Toth, R. / Sundaramoorthy, R. / Knebel, A. / 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 | 5n38.cif.gz | 197.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5n38.ent.gz | 156.4 KB | Display | PDB format |
PDBx/mmJSON format | 5n38.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5n38_validation.pdf.gz | 454.4 KB | Display | wwPDB validaton report |
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Full document | 5n38_full_validation.pdf.gz | 458.7 KB | Display | |
Data in XML | 5n38_validation.xml.gz | 18.4 KB | Display | |
Data in CIF | 5n38_validation.cif.gz | 25.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n3/5n38 ftp://data.pdbj.org/pub/pdb/validation_reports/n3/5n38 | HTTPS FTP |
-Related structure data
Related structure data | 5n2wC 5c1zS 5cawS 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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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: 45628.035 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PARK2, PRKN / Production host: Escherichia coli (E. coli) References: UniProt: O60260, Transferases; Acyltransferases; Aminoacyltransferases |
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#2: Protein | Mass: 8640.854 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Ser65 is phosphorylated / Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47 |
-Non-polymers , 4 types, 65 molecules
#3: Chemical | ChemComp-PEG / | ||
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#4: Chemical | ChemComp-CL / | ||
#5: Chemical | ChemComp-ZN / #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.3 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 100mM Tris pH 8.5, 200mM TMAO, PEG MME 2000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9793 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 16, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→72.56 Å / Num. obs: 17000 / % possible obs: 96.4 % / Redundancy: 3.5 % / Biso Wilson estimate: 63.57 Å2 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 2.6→2.76 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.2 / CC1/2: 0.64 / % possible all: 88.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5C1Z, 5CAW Resolution: 2.6→72.56 Å / Cor.coef. Fo:Fc: 0.9357 / Cor.coef. Fo:Fc free: 0.9141 / SU R Cruickshank DPI: 0.595 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.686 / SU Rfree Blow DPI: 0.288 / SU Rfree Cruickshank DPI: 0.286
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Displacement parameters | Biso mean: 53.75 Å2
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Refine analyze | Luzzati coordinate error obs: 0.347 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.6→72.56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Total num. of bins used: 9
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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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