+Open data
-Basic information
Entry | Database: PDB / ID: 8ept | ||||||||||||
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Title | UBE3A isoform 2 AZUL domain | ||||||||||||
Components | Ubiquitin-protein ligase E3A | ||||||||||||
Keywords | LIGASE / ubiquitin ligase / proteasome interaction | ||||||||||||
Function / homology | Function and homology information sperm entry / positive regulation of Golgi lumen acidification / negative regulation of dendritic spine morphogenesis / motor learning / regulation of ubiquitin-dependent protein catabolic process / prostate gland growth / HECT-type E3 ubiquitin transferase / progesterone receptor signaling pathway / locomotory exploration behavior / androgen receptor signaling pathway ...sperm entry / positive regulation of Golgi lumen acidification / negative regulation of dendritic spine morphogenesis / motor learning / regulation of ubiquitin-dependent protein catabolic process / prostate gland growth / HECT-type E3 ubiquitin transferase / progesterone receptor signaling pathway / locomotory exploration behavior / androgen receptor signaling pathway / protein K48-linked ubiquitination / protein autoubiquitination / ovarian follicle development / negative regulation of TORC1 signaling / cellular response to brain-derived neurotrophic factor stimulus / proteasome complex / response to cocaine / positive regulation of protein ubiquitination / response to progesterone / regulation of circadian rhythm / brain development / response to hydrogen peroxide / regulation of synaptic plasticity / protein polyubiquitination / rhythmic process / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription coactivator activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / glutamatergic synapse / positive regulation of transcription by RNA polymerase II / proteolysis / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | SOLUTION NMR / simulated annealing | ||||||||||||
Authors | Bregnard, T.A. / Bezsonova, I. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: To Be Published Title: Differences in structure, dynamics and Zn-coordination between isoforms of human ubiquitin ligase UBE3A Authors: Bregnard, T.A. / Fairchild, D. / Chen, X. / Erlandsen, H. / Walters, K.J. / Korzhnev, D.M. / Bezsonova, I. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ept.cif.gz | 543.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ept.ent.gz | 455.6 KB | Display | PDB format |
PDBx/mmJSON format | 8ept.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ept_validation.pdf.gz | 468.3 KB | Display | wwPDB validaton report |
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Full document | 8ept_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8ept_validation.xml.gz | 191.4 KB | Display | |
Data in CIF | 8ept_validation.cif.gz | 127.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ep/8ept ftp://data.pdbj.org/pub/pdb/validation_reports/ep/8ept | HTTPS FTP |
-Related structure data
Related structure data | 8enpC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 10217.599 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UBE3A, E6AP, EPVE6AP, HPVE6A / Plasmid: pET28b+ / Production host: Escherichia coli BL21 (bacteria) References: UniProt: Q05086, HECT-type E3 ubiquitin transferase |
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#2: Chemical | ChemComp-ZN / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: solution Contents: 1.8 mM [U-99% 13C; U-99% 15N] UBE3A iso2 AZUL, 10 mM MOPS, 450 mM sodium chloride, 10 mM beta-mercaptoethanol, 10 uM zinc sulfate, 90% H2O/10% D2O Label: UBE3A AZUL iso2 1 / Solvent system: 90% H2O/10% D2O | ||||||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 450 mM / Label: structure conditions / pH: 6 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Agilent VNMRS / Manufacturer: Agilent / Model: VNMRS / Field strength: 800 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 5 / Details: CNS refinement in explicit water | ||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 10000 / Conformers submitted total number: 20 |