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Yorodumi- PDB-2did: One sequence two fold ? : Correct fold of the zf-B-box domain fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2did | ||||||
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Title | One sequence two fold ? : Correct fold of the zf-B-box domain from human tripartite motif protein 39 | ||||||
Components | Tripartite motif protein 39 | ||||||
Keywords | PROTEIN BINDING / zf-B-box domian / Zn binding / one sequence two fold / NPPSFA / National Project on Protein Structural and Functional Analyses / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information regulation of cell cycle G1/S phase transition / mitotic G2 DNA damage checkpoint signaling / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of canonical NF-kappaB signal transduction / negative regulation of ubiquitin-dependent protein catabolic process / positive regulation of apoptotic signaling pathway / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / protein stabilization ...regulation of cell cycle G1/S phase transition / mitotic G2 DNA damage checkpoint signaling / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of canonical NF-kappaB signal transduction / negative regulation of ubiquitin-dependent protein catabolic process / positive regulation of apoptotic signaling pathway / RING-type E3 ubiquitin transferase / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / protein stabilization / protein ubiquitination / apoptotic process / mitochondrion / zinc ion binding / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics, restrained molecular dynamics | ||||||
Authors | Tomizawa, T. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: One sequence two fold ? : Correct fold of the zf-B-box domain from human tripartite motif protein 39 Authors: Tomizawa, T. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2did.cif.gz | 292 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2did.ent.gz | 242.3 KB | Display | PDB format |
PDBx/mmJSON format | 2did.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2did_validation.pdf.gz | 339.9 KB | Display | wwPDB validaton report |
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Full document | 2did_full_validation.pdf.gz | 460.5 KB | Display | |
Data in XML | 2did_validation.xml.gz | 17.8 KB | Display | |
Data in CIF | 2did_validation.cif.gz | 28.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/di/2did ftp://data.pdbj.org/pub/pdb/validation_reports/di/2did | 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: 5500.058 Da / Num. of mol.: 1 / Fragment: zf-B-box domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: TRIM39 / Plasmid: P050302-55 / Production host: Cell free synthesis / References: UniProt: Q9HCM9 |
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#2: Chemical |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 1.28mM zf-B-box domain U-15N, 13C; 20mM d-Tris-HCl(pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 50uM ZnCl2; 1mM IDA; 90% H2O, 10% D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 120mM / pH: 7.0 / Pressure: ambient / Temperature: 296 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics, restrained molecular dynamics Software ordinal: 1 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function, structures with the lowest energy, structures with the least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 20 |