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Yorodumi- PDB-2yuc: Solution structure of the TRAF-type zinc finger domains (102-164)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yuc | ||||||
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Title | Solution structure of the TRAF-type zinc finger domains (102-164) from human TNF receptor associated factor 4 | ||||||
Components | TNF receptor-associated factor 4 | ||||||
Keywords | SIGNALING PROTEIN / zf-TRAF / Cysteine-rich domain associated with RING and Traf domains protein 1 / Malignant 62 / RING finger protein 83 / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information respiratory tube development / WW domain binding / respiratory gaseous exchange by respiratory system / thioesterase binding / tumor necrosis factor receptor binding / regulation of canonical NF-kappaB signal transduction / bicellular tight junction / positive regulation of protein kinase activity / positive regulation of JNK cascade / RING-type E3 ubiquitin transferase ...respiratory tube development / WW domain binding / respiratory gaseous exchange by respiratory system / thioesterase binding / tumor necrosis factor receptor binding / regulation of canonical NF-kappaB signal transduction / bicellular tight junction / positive regulation of protein kinase activity / positive regulation of JNK cascade / RING-type E3 ubiquitin transferase / fibrillar center / transferase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / regulation of apoptotic process / cytoskeleton / innate immune response / ubiquitin protein ligase binding / protein kinase binding / apoptotic process / perinuclear region of cytoplasm / signal transduction / zinc ion binding / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Hayashi, F. / Suetake, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution structure of the TRAF-type zinc finger domains (102-164) from human TNF receptor associated factor 4 Authors: Hayashi, F. / Suetake, 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 | 2yuc.cif.gz | 428.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yuc.ent.gz | 356.1 KB | Display | PDB format |
PDBx/mmJSON format | 2yuc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2yuc_validation.pdf.gz | 343.9 KB | Display | wwPDB validaton report |
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Full document | 2yuc_full_validation.pdf.gz | 495.7 KB | Display | |
Data in XML | 2yuc_validation.xml.gz | 30.4 KB | Display | |
Data in CIF | 2yuc_validation.cif.gz | 46.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yu/2yuc ftp://data.pdbj.org/pub/pdb/validation_reports/yu/2yuc | HTTPS FTP |
-Related structure data
Similar structure data | |
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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: 8228.226 Da / Num. of mol.: 1 / Fragment: TRAF-type zinc finger domains Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: cell free protein synthesis / Gene: TRAF4 / Plasmid: P050404-07 / References: UniProt: Q9BUZ4 |
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#2: Chemical |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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NMR details | Text: The structure was determined using triple-resonance NMR spectroscopy. |
-Sample preparation
Details | Contents: 1.24mM U-15N, 13C-labeled protein; 20mM d-Tris-HCl; 100mM NaCl; 1mM DTT; 0.02% NaN3; 0.05mM ZnCl2; 1mM IDA, 90% H2O, 10%D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 120mM / pH: 7 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 1 Details: The structures are based on a total of 918 restraints, 870 are NOE-derived distance constraints, 48 dihedral angle restraints. | ||||||||||||||||||||||||||||
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 |