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Yorodumi- PDB-7p2k: Solution NMR Structure of Arginine to Cysteine mutant of Arkadia ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7p2k | |||||||||
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Title | Solution NMR Structure of Arginine to Cysteine mutant of Arkadia RING domain. | |||||||||
Components | E3 ubiquitin-protein ligase Arkadia | |||||||||
Keywords | LIGASE / Arkadia / Rnf111 / E3 Ubiquitin ligase / RING domain / Arginine / TGF-b / UbcH5b | |||||||||
Function / homology | Function and homology information SUMO polymer binding / global genome nucleotide-excision repair / pattern specification process / positive regulation of transforming growth factor beta receptor signaling pathway / SMAD binding / positive regulation of protein ubiquitination / Downregulation of SMAD2/3:SMAD4 transcriptional activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / RING-type E3 ubiquitin transferase / PML body ...SUMO polymer binding / global genome nucleotide-excision repair / pattern specification process / positive regulation of transforming growth factor beta receptor signaling pathway / SMAD binding / positive regulation of protein ubiquitination / Downregulation of SMAD2/3:SMAD4 transcriptional activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / RING-type E3 ubiquitin transferase / PML body / Formation of Incision Complex in GG-NER / protein polyubiquitination / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-dependent protein catabolic process / protein ubiquitination / positive regulation of DNA-templated transcription / protein-containing complex / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | SOLUTION NMR / molecular dynamics | |||||||||
Authors | Raptis, V. / Marousis, K.D. / Birkou, M. / Bentrop, D. / Episkopou, V. / Spyroulias, G.A. | |||||||||
Funding support | European Union, 2items
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Citation | Journal: Front Mol Biosci / Year: 2022 Title: Impact of a Single Nucleotide Polymorphism on the 3D Protein Structure and Ubiquitination Activity of E3 Ubiquitin Ligase Arkadia. Authors: Birkou, M. / Raptis, V. / Marousis, K.D. / Tsevis, A. / Bourikas, K. / Bentrop, D. / Episkopou, V. / Spyroulias, G.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7p2k.cif.gz | 697.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7p2k.ent.gz | 595.3 KB | Display | PDB format |
PDBx/mmJSON format | 7p2k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p2/7p2k ftp://data.pdbj.org/pub/pdb/validation_reports/p2/7p2k | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 7905.983 Da / Num. of mol.: 1 / Mutation: R957C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RNF111 / Plasmid: pGex-47-1 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q6ZNA4, RING-type E3 ubiquitin transferase | ||
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#2: Chemical | 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 |
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Sample |
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Sample conditions | Ionic strength: 50 mM / Label: Conditions_1 / pH: 7 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: molecular dynamics / Software ordinal: 3 | ||||||||||||||||||||
NMR representative | Selection criteria: target function | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 400 / Conformers submitted total number: 30 |