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Yorodumi- PDB-2egp: Solution structure of the RING-finger domain from human Tripartit... -
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-Basic information
Entry | Database: PDB / ID: 2egp | ||||||
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Title | Solution structure of the RING-finger domain from human Tripartite motif protein 34 | ||||||
Components | Tripartite motif-containing protein 34 | ||||||
Keywords | ANTIVIRAL PROTEIN / zf-C3HC4 domain / Tripartite motif protein 34 / Interferon-responsive finger protein 1 / RING finger protein 21 / TRIM34 / IFP1 / RNF21 / 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 viral entry into host cell / type II interferon-mediated signaling pathway / positive regulation of autophagy / positive regulation of DNA-binding transcription factor activity / protein polyubiquitination / Interferon gamma signaling / ubiquitin protein ligase activity / positive regulation of NF-kappaB transcription factor activity / regulation of protein localization / regulation of gene expression ...regulation of viral entry into host cell / type II interferon-mediated signaling pathway / positive regulation of autophagy / positive regulation of DNA-binding transcription factor activity / protein polyubiquitination / Interferon gamma signaling / ubiquitin protein ligase activity / positive regulation of NF-kappaB transcription factor activity / regulation of protein localization / regulation of gene expression / defense response to virus / positive regulation of canonical NF-kappaB signal transduction / protein ubiquitination / innate immune response / protein kinase binding / protein homodimerization activity / zinc ion binding / nucleoplasm / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Inoue, K. / Hayashi, F. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution structure of the RING-finger domain from human Tripartite motif protein 34 Authors: Inoue, K. / Hayashi, F. / Yokoyama, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2egp.cif.gz | 440.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2egp.ent.gz | 366.2 KB | Display | PDB format |
PDBx/mmJSON format | 2egp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2egp_validation.pdf.gz | 340.3 KB | Display | wwPDB validaton report |
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Full document | 2egp_full_validation.pdf.gz | 455.5 KB | Display | |
Data in XML | 2egp_validation.xml.gz | 23.6 KB | Display | |
Data in CIF | 2egp_validation.cif.gz | 38 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eg/2egp ftp://data.pdbj.org/pub/pdb/validation_reports/eg/2egp | 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: 8248.277 Da / Num. of mol.: 1 / Fragment: zf-C3HC4 domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: TRIM34, IFP1, RNF21 / Plasmid: P060327-02 / References: UniProt: Q9BYJ4 |
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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: 1.40mM U-15N,13C-labeled protein; 20mM d-Tris-HCl; 100mM NaCl; 1mM d-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 | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations,structures with the lowest energy,target function Conformers calculated total number: 100 / Conformers submitted total number: 20 |