+Open data
-Basic information
Entry | Database: PDB / ID: 1s4g | ||||||
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Title | Somatomedin-B Domain of human plasma vitronectin. | ||||||
Components | Vitronectin | ||||||
Keywords | CELL ADHESION / Somatomedin B domain / disulfide knot / vitronectin | ||||||
Function / homology | Function and homology information rough endoplasmic reticulum lumen / smooth muscle cell-matrix adhesion / peptidase inhibitor complex / alphav-beta3 integrin-vitronectin complex / scavenger receptor activity / negative regulation of endopeptidase activity / protein complex involved in cell-matrix adhesion / negative regulation of blood coagulation / extracellular matrix binding / positive regulation of vascular endothelial growth factor receptor signaling pathway ...rough endoplasmic reticulum lumen / smooth muscle cell-matrix adhesion / peptidase inhibitor complex / alphav-beta3 integrin-vitronectin complex / scavenger receptor activity / negative regulation of endopeptidase activity / protein complex involved in cell-matrix adhesion / negative regulation of blood coagulation / extracellular matrix binding / positive regulation of vascular endothelial growth factor receptor signaling pathway / positive regulation of cell-substrate adhesion / Molecules associated with elastic fibres / cell adhesion mediated by integrin / extracellular matrix structural constituent / Syndecan interactions / polysaccharide binding / positive regulation of wound healing / positive regulation of smooth muscle cell migration / oligodendrocyte differentiation / endodermal cell differentiation / protein polymerization / basement membrane / ECM proteoglycans / Integrin cell surface interactions / negative regulation of fibrinolysis / regulation of cell adhesion / collagen binding / extracellular matrix organization / cell-matrix adhesion / liver regeneration / Regulation of Complement cascade / Golgi lumen / positive regulation of receptor-mediated endocytosis / cell migration / positive regulation of peptidyl-tyrosine phosphorylation / integrin binding / heparin binding / positive regulation of protein binding / collagen-containing extracellular matrix / blood microparticle / cell adhesion / immune response / intracellular membrane-bounded organelle / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Mayasundari, A. / Whittemore, N.A. / Serpersu, E.H. / Peterson, C.B. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: The solution structure of the N-terminal domain of human vitronectin: proximal sites that regulate fibrinolysis and cell migration Authors: Mayasundari, A. / Whittemore, N.A. / Serpersu, E.H. / Peterson, C.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1s4g.cif.gz | 297 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1s4g.ent.gz | 255.1 KB | Display | PDB format |
PDBx/mmJSON format | 1s4g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s4/1s4g ftp://data.pdbj.org/pub/pdb/validation_reports/s4/1s4g | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 5824.493 Da / Num. of mol.: 1 / Fragment: Somatomedin B / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: plasma / References: UniProt: P04004 |
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#2: Chemical | ChemComp-OH / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: Isolated from human plasma vitronectin by CNBr cleavage |
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Sample conditions | Ionic strength: low / pH: 4.4 / Temperature: 298 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz |
-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: NOE cross-peak intensities were converted into distance restraints as follows: strong, 1.8-2.7 ; medium, 1.8-3.4 ; weak, 1.8-4.5 , and very weak 1.8-6.0. An additional 1.0 was added to upper ...Details: NOE cross-peak intensities were converted into distance restraints as follows: strong, 1.8-2.7 ; medium, 1.8-3.4 ; weak, 1.8-4.5 , and very weak 1.8-6.0. An additional 1.0 was added to upper limits involving methyl protons, 0.5 for methylene protons and 2.3 for degenerate Hd and He protons of tyrosines and phenylalanines. Also, a 0.2 was added to the upper limits of NOEs involving amide protons. Backbone F angles were restrained to -120 50 for 3JHNHa = 8-9 Hz, and -120 40 for JHNHa > 9Hz. A restraint of 100 80 was also applied to F angle for residues that show stronger NHi-Hai-1 NOE than the intraresidue NH-Ha NOE. A total of 329 NOE restraints and 18 F restraints were used in structure determination. Random structures were generated by subjecting the peptide to an initial 10000-step minimization at 298K. The temperature was then raised gradually to 1000K during a 1000 step dynamics simulation. The peptide was subjected to minimization and a 10ps dynamics at 1000K. The NMR-derived restraints were then imposed on the peptide and the peptide was slowly annealed to 298K in a 100ps trajectory. Finally, the structures were subjected to further minimization at 298K. The force constant for the distance restraints was 100 kcal/mol 2 and the dielectric constant was 4. | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with favorable non-bond energy Conformers calculated total number: 60 / Conformers submitted total number: 20 |