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Yorodumi- PDB-2rru: Solution structure of the UBA omain of p62 and its interaction wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2rru | ||||||
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Title | Solution structure of the UBA omain of p62 and its interaction with ubiquitin | ||||||
Components | Sequestosome-1 | ||||||
Keywords | PROTEIN BINDING / UBIQUITIN / UBA DOMAIN / P62/SQSTM1 / Autophagy | ||||||
Function / homology | Function and homology information Pexophagy / NRIF signals cell death from the nucleus / p75NTR recruits signalling complexes / brown fat cell proliferation / protein localization to perinuclear region of cytoplasm / PINK1-PRKN Mediated Mitophagy / protein targeting to vacuole involved in autophagy / Lewy body / NF-kB is activated and signals survival / response to mitochondrial depolarisation ...Pexophagy / NRIF signals cell death from the nucleus / p75NTR recruits signalling complexes / brown fat cell proliferation / protein localization to perinuclear region of cytoplasm / PINK1-PRKN Mediated Mitophagy / protein targeting to vacuole involved in autophagy / Lewy body / NF-kB is activated and signals survival / response to mitochondrial depolarisation / aggrephagy / amphisome / negative regulation of toll-like receptor 4 signaling pathway / Interleukin-1 signaling / KEAP1-NFE2L2 pathway / pexophagy / regulation of protein complex stability / endosome organization / non-membrane-bounded organelle assembly / phagophore assembly site / aggresome / regulation of canonical NF-kappaB signal transduction / ubiquitin-modified protein reader activity / autolysosome / K63-linked polyubiquitin modification-dependent protein binding / intracellular non-membrane-bounded organelle / temperature homeostasis / immune system process / mitophagy / autophagosome / positive regulation of autophagy / energy homeostasis / signaling adaptor activity / sperm midpiece / negative regulation of protein ubiquitination / protein sequestering activity / sarcomere / SH2 domain binding / molecular condensate scaffold activity / ubiquitin binding / positive regulation of long-term synaptic potentiation / response to ischemia / macroautophagy / protein kinase C binding / positive regulation of protein localization to plasma membrane / transcription coregulator activity / ionotropic glutamate receptor binding / P-body / protein catabolic process / PML body / autophagy / protein import into nucleus / late endosome / protein-macromolecule adaptor activity / signaling receptor activity / transcription by RNA polymerase II / cell differentiation / positive regulation of protein phosphorylation / apoptotic process / ubiquitin protein ligase binding / protein-containing complex binding / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / mitochondrion / zinc ion binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | SOLUTION NMR / DGSA-distance geometry simulated annealing, DGSA-DISTANCE GEOMETRY SIMULATE ANNEALING | ||||||
Model details | lowest energy, model 1 | ||||||
Authors | Isogai, S. / Morimoto, D. / Arita, K. / Unzai, S. / Tenno, T. / Hasegawa, J. / Sou, Y. / Komatsu, M. / Tanaka, K. / Shirakawa, M. / Tochio, H. | ||||||
Citation | Journal: To be Published Title: Crystal structure of the UBA omain of p62 and its interaction with ubiquitin Authors: Isogai, S. / Morimoto, D. / Arita, K. / Unzai, S. / Tenno, T. / Sou, Y. / Komatsu, M. / Tanaka, K. / Shirakawa, M. / Tochio, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2rru.cif.gz | 363.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2rru.ent.gz | 306.2 KB | Display | PDB format |
PDBx/mmJSON format | 2rru.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2rru_validation.pdf.gz | 465.8 KB | Display | wwPDB validaton report |
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Full document | 2rru_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 2rru_validation.xml.gz | 115.1 KB | Display | |
Data in CIF | 2rru_validation.cif.gz | 82.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rr/2rru ftp://data.pdbj.org/pub/pdb/validation_reports/rr/2rru | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data | |
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: 5817.500 Da / Num. of mol.: 1 / Fragment: UBA domain (UNP RESIDUES 393-438) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: SQSTM1, A170, STAP / Production host: Escherichia coli (E. coli) / References: UniProt: Q64337 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 0.4 mM [U-95% 13C; U-95% 15N] P62/SEQUESTOSOME-1-1, 2.4 mM Ubiquitin-2, 10 % [U-2H] D2O-3, 20 mM potassium phosphate-4, 5 mM potassium chloride-5, 1 mM EDTA-6, 10 % D2O-7, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O | ||||||||||||||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 0.025 / pH: 6.8 / Pressure: AMBIENT / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: BRUKER AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 700 MHz |
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-Processing
NMR software |
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Refinement | Method: DGSA-distance geometry simulated annealing, DGSA-DISTANCE GEOMETRY SIMULATE ANNEALING Software ordinal: 1 | ||||||||||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: STRUCTURES WITH THE LOWEST ENER Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1 |