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Yorodumi- PDB-2dmv: Solution structure of the second ww domain of Itchy homolog E3 ub... -
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-Basic information
Entry | Database: PDB / ID: 2dmv | ||||||
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Title | Solution structure of the second ww domain of Itchy homolog E3 ubiquitin protein ligase (Itch) | ||||||
Components | Itchy homolog E3 ubiquitin protein ligase | ||||||
Keywords | LIGASE / WW domain / three stranded antiparallel beta sheet / 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 protein deubiquitination / negative regulation of cytoplasmic pattern recognition receptor signaling pathway / ubiquitin-like protein transferase activity / negative regulation of defense response to virus / protein K29-linked ubiquitination / nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / T cell anergy / positive regulation of T cell anergy / CXCR chemokine receptor binding / regulation of necroptotic process ...regulation of protein deubiquitination / negative regulation of cytoplasmic pattern recognition receptor signaling pathway / ubiquitin-like protein transferase activity / negative regulation of defense response to virus / protein K29-linked ubiquitination / nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway / T cell anergy / positive regulation of T cell anergy / CXCR chemokine receptor binding / regulation of necroptotic process / CD4-positive, alpha-beta T cell proliferation / negative regulation of CD4-positive, alpha-beta T cell proliferation / negative regulation of JNK cascade / HECT-type E3 ubiquitin transferase / arrestin family protein binding / regulation of hematopoietic stem cell differentiation / negative regulation of type I interferon production / positive regulation of receptor catabolic process / negative regulation of NF-kappaB transcription factor activity / ubiquitin-like protein ligase binding / protein monoubiquitination / ligase activity / protein K63-linked ubiquitination / protein autoubiquitination / protein K48-linked ubiquitination / ribonucleoprotein complex binding / Downregulation of ERBB4 signaling / Activated NOTCH1 Transmits Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / regulation of cell growth / Degradation of GLI1 by the proteasome / Hedgehog 'on' state / NOD1/2 Signaling Pathway / Regulation of necroptotic cell death / receptor internalization / positive regulation of protein catabolic process / ubiquitin-protein transferase activity / SARS-CoV-1 activates/modulates innate immune responses / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / cell cortex / early endosome membrane / cytoplasmic vesicle / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / defense response to virus / protein ubiquitination / inflammatory response / symbiont entry into host cell / intracellular membrane-bounded organelle / innate immune response / apoptotic process / negative regulation of apoptotic process / protein-containing complex / mitochondrion / extracellular exosome / nucleoplasm / membrane / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Ohnishi, S. / Paakkonen, K. / Tochio, N. / Tomizawa, T. / Koshiba, S. / Inoue, M. / Guntert, P. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution structure of the second ww domain of Itchy homolog E3 ubiquitin protein ligase (Itch) Authors: Ohnishi, S. / Paakkonen, K. / Tochio, N. / Tomizawa, T. / Koshiba, S. / Inoue, M. / Guntert, P. / 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 | 2dmv.cif.gz | 249.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dmv.ent.gz | 208.5 KB | Display | PDB format |
PDBx/mmJSON format | 2dmv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2dmv_validation.pdf.gz | 338.9 KB | Display | wwPDB validaton report |
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Full document | 2dmv_full_validation.pdf.gz | 427.3 KB | Display | |
Data in XML | 2dmv_validation.xml.gz | 12.9 KB | Display | |
Data in CIF | 2dmv_validation.cif.gz | 21 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dm/2dmv ftp://data.pdbj.org/pub/pdb/validation_reports/dm/2dmv | 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/peptide | Mass: 4720.034 Da / Num. of mol.: 1 / Fragment: WW domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: ITCH / Plasmid: P050620-31 / Production host: Cell free synthesis References: UniProt: Q96J02, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
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NMR experiment |
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NMR details | Text: Information from residual dipolar couplings was used in the structural calculation. |
-Sample preparation
Details | Contents: 1.4mM protein U-15N, 13C; 20mM d-Tris-HCl(pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O, 90% H2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 120mM / pH: 7.0 / Pressure: ambient / Temperature: 298 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 / 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 |