+Open data
-Basic information
Entry | Database: PDB / ID: 2kiz | ||||||
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Title | Solution structure of Arkadia RING-H2 finger domain | ||||||
Components | E3 ubiquitin-protein ligase Arkadia | ||||||
Keywords | METAL BINDING PROTEIN / ARKADIA / RING-H2 FINGER / E3 LIGASE / ZN BINDING DOMAIN / Metal-binding / Zinc-finger | ||||||
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 / protein-containing complex / nucleoplasm / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Model type details | minimized average | ||||||
Authors | Kandias, N.G. / Chasapis, C.T. / Bentrop, D. / Episkopou, V. / Spyroulias, G.A. | ||||||
Citation | Journal: Proteins / Year: 2012 Title: NMR-based insights into the conformational and interaction properties of Arkadia RING-H2 E3 Ub ligase. Authors: Chasapis, C.T. / Kandias, N.G. / Episkopou, V. / Bentrop, D. / Spyroulias, G.A. #1: Journal: Biochem.Biophys.Res.Commun. / Year: 2009 Title: High yield expression and NMR characterization of Arkadia E3 ubiquitin ligase RING-H2 finger domain. Authors: Kandias, N.G. / Chasapis, C.T. / 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 | 2kiz.cif.gz | 728.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2kiz.ent.gz | 640.7 KB | Display | PDB format |
PDBx/mmJSON format | 2kiz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2kiz_validation.pdf.gz | 364.3 KB | Display | wwPDB validaton report |
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Full document | 2kiz_full_validation.pdf.gz | 540 KB | Display | |
Data in XML | 2kiz_validation.xml.gz | 31.3 KB | Display | |
Data in CIF | 2kiz_validation.cif.gz | 56.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ki/2kiz ftp://data.pdbj.org/pub/pdb/validation_reports/ki/2kiz | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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-Links
-Assembly
Deposited unit |
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NMR ensembles |
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-Components
#1: Protein | Mass: 7960.034 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RNF111 / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / References: UniProt: Q6ZNA4 |
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#2: Chemical |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR / Details: Recombinant RING finger polypeptide (RING-H2 type) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 1.0 mM [U-98% 13C; U-98% 15N] RING Finger monomer, 50 mM Pi, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O | ||||||||||||
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Sample |
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Sample conditions | Ionic strength: 50 / pH: 6.9 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker Avance / Manufacturer: Bruker / Model: Avance / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 1 | ||||||||||||
NMR representative | Selection criteria: minimized average structure | ||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 31 / Conformers submitted total number: 31 |