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Yorodumi- PDB-1x5b: The solution structure of the VHS domain of human Signal transduc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1x5b | ||||||
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Title | The solution structure of the VHS domain of human Signal transducing adaptor molecule 2 | ||||||
Components | signal transducing adaptor molecule 2 | ||||||
Keywords | PROTEIN BINDING / VHS domain / ubiquitin binding / STAM2 / structural genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI | ||||||
Function / homology | Function and homology information ESCRT-0 complex / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / membrane fission / multivesicular body assembly / RHOU GTPase cycle / endocytic vesicle / Endosomal Sorting Complex Required For Transport (ESCRT) / phosphatidylinositol binding / InlB-mediated entry of Listeria monocytogenes into host cell / ubiquitin binding ...ESCRT-0 complex / protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway / membrane fission / multivesicular body assembly / RHOU GTPase cycle / endocytic vesicle / Endosomal Sorting Complex Required For Transport (ESCRT) / phosphatidylinositol binding / InlB-mediated entry of Listeria monocytogenes into host cell / ubiquitin binding / EGFR downregulation / macroautophagy / Negative regulation of MET activity / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / early endosome membrane / Ub-specific processing proteases / intracellular membrane-bounded organelle / signal transduction / nucleoplasm / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Tochio, N. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: The solution structure of the VHS domain of human Signal transducing adaptor molecule 2 Authors: Tochio, N. / Koshiba, S. / Inoue, M. / 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 | 1x5b.cif.gz | 950.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1x5b.ent.gz | 799.1 KB | Display | PDB format |
PDBx/mmJSON format | 1x5b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x5/1x5b ftp://data.pdbj.org/pub/pdb/validation_reports/x5/1x5b | HTTPS FTP |
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-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: 17685.221 Da / Num. of mol.: 1 / Fragment: VHS domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: STAM2 / Plasmid: P040607-06 / References: UniProt: O75886 |
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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: 1.5mM VHS domain U-15N,13C; 20mM d-Tris HCl; 100mM NaCl; 5mM d-DTT; 0.02% NaN3; 10% D2O Solvent system: 90% H2O/10% D2O |
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Sample conditions | Ionic strength: 120mM / pH: 7.0 / Pressure: ambient / Temperature: 296 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 900 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 least restraint violations Conformers calculated total number: 100 / Conformers submitted total number: 20 |