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Yorodumi- PDB-2yt6: Solution structure of the SH3_1 domain of Yamaguchi sarcoma viral... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yt6 | ||||||
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Title | Solution structure of the SH3_1 domain of Yamaguchi sarcoma viral (v-yes) oncogene homolog 1 | ||||||
Components | Adult male urinary bladder cDNA, RIKEN full-length enriched library, clone:9530076O17 product:Yamaguchi sarcoma viral (v-yes) oncogene homolog | ||||||
Keywords | CELL CYCLE / SH3_1 domain / Yamaguchi sarcoma viral (v-yes) oncogene homolog 1 / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information PECAM1 interactions / CTLA4 inhibitory signaling / Signaling by ERBB2 / CD28 co-stimulation / Regulation of KIT signaling / EPHA-mediated growth cone collapse / EPH-ephrin mediated repulsion of cells / EPHB-mediated forward signaling / Signaling by SCF-KIT / FCGR activation ...PECAM1 interactions / CTLA4 inhibitory signaling / Signaling by ERBB2 / CD28 co-stimulation / Regulation of KIT signaling / EPHA-mediated growth cone collapse / EPH-ephrin mediated repulsion of cells / EPHB-mediated forward signaling / Signaling by SCF-KIT / FCGR activation / regulation of D-glucose transmembrane transport / Regulation of signaling by CBL / epidermal growth factor receptor binding / postsynaptic specialization, intracellular component / extrinsic component of cytoplasmic side of plasma membrane / cellular response to platelet-derived growth factor stimulus / cellular response to retinoic acid / cell surface receptor protein tyrosine kinase signaling pathway / cellular response to transforming growth factor beta stimulus / phosphotyrosine residue binding / actin filament / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / positive regulation of peptidyl-tyrosine phosphorylation / protein tyrosine kinase activity / transmembrane transporter binding / cell differentiation / innate immune response / signaling receptor binding / centrosome / glutamatergic synapse / Golgi apparatus / enzyme binding / positive regulation of transcription by RNA polymerase II / ATP binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Dang, W. / Muto, Y. / Inoue, M. / Kigawa, T. / Shirouzu, M. / Tarada, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Solution structure of the SH3_1 domain of Yamaguchi sarcoma viral (v-yes) oncogene homolog 1 Authors: Dang, W. / Muto, Y. / Inoue, M. / Kigawa, T. / Shirouzu, M. / Tarada, T. / Yokoyama, S. | ||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR DETERMINED | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR DETERMINED |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yt6.cif.gz | 615.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yt6.ent.gz | 516.2 KB | Display | PDB format |
PDBx/mmJSON format | 2yt6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2yt6_validation.pdf.gz | 344.3 KB | Display | wwPDB validaton report |
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Full document | 2yt6_full_validation.pdf.gz | 492.9 KB | Display | |
Data in XML | 2yt6_validation.xml.gz | 40.4 KB | Display | |
Data in CIF | 2yt6_validation.cif.gz | 62.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yt/2yt6 ftp://data.pdbj.org/pub/pdb/validation_reports/yt/2yt6 | 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: 11635.558 Da / Num. of mol.: 1 / Fragment: SH3_1 domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Description: cell-free protein synthesis / Gene: Yes1 / Plasmid: P050822-05 / References: UniProt: Q8CBP1, UniProt: Q04736*PLUS |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 1.0mM 13C, 15N-labeled protein; 20mM d-Tris-HCl (pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 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: 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: structures with the least restraint violations, structures with the lowest energy, target function Conformers calculated total number: 100 / Conformers submitted total number: 20 |