[English] 日本語
Yorodumi- PDB-2ecj: Solution structure of the RING domain of the human tripartite mot... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ecj | ||||||
---|---|---|---|---|---|---|---|
Title | Solution structure of the RING domain of the human tripartite motif-containing protein 39 | ||||||
Components | Tripartite motif-containing protein 39 | ||||||
Keywords | METAL BINDING PROTEIN / Tripartite motif-containing protein 39 / TRIM39 / RING domain / zinc-binding domain / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / 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 | ||||||
Authors | Miyamoto, K. / Sato, M. / Koshiba, S. / Watanabe, S. / Harada, T. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution structure of the RING domain of the human tripartite motif-containing protein 39 Authors: Miyamoto, K. / Sato, M. / Koshiba, S. / Watanabe, S. / Harada, T. / Kigawa, T. / Yokoyama, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2ecj.cif.gz | 341.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2ecj.ent.gz | 281.9 KB | Display | PDB format |
PDBx/mmJSON format | 2ecj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ecj_validation.pdf.gz | 341.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2ecj_full_validation.pdf.gz | 475.3 KB | Display | |
Data in XML | 2ecj_validation.xml.gz | 21.2 KB | Display | |
Data in CIF | 2ecj_validation.cif.gz | 32.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ec/2ecj ftp://data.pdbj.org/pub/pdb/validation_reports/ec/2ecj | HTTPS FTP |
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
NMR ensembles |
|
-Components
#1: Protein | Mass: 6429.298 Da / Num. of mol.: 1 / Fragment: RING domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: TRIM39 / Plasmid: P060828-17 / References: UniProt: Q9HCM9 |
---|---|
#2: Chemical |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
NMR experiment |
|
-Sample preparation
Details | Contents: 1.06mM RING domain U-13C, 15N; 20mM d-Tris-HCl(pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 0.05mM ZNCl2; 1.0mM IDA; 90% H2O, 10% D2O Solvent system: 90% H2O/10% D2O |
---|---|
Sample conditions | Ionic strength: 120 / pH: 7.0 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz |
---|
-Processing
NMR software |
| ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method: torsion angle dynamics / Software ordinal: 1 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations, target function Conformers calculated total number: 100 / Conformers submitted total number: 20 |