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Yorodumi- PDB-2tgi: CRYSTAL STRUCTURE OF TRANSFORMING GROWTH FACTOR-BETA2: AN UNUSUAL... -
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-Basic information
Entry | Database: PDB / ID: 2tgi | ||||||
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Title | CRYSTAL STRUCTURE OF TRANSFORMING GROWTH FACTOR-BETA2: AN UNUSUAL FOLD FOR THE SUPERFAMILY | ||||||
Components | TRANSFORMING GROWTH FACTOR ,BETA 2 | ||||||
Keywords | GROWTH FACTOR | ||||||
Function / homology | Function and homology information regulation of timing of catagen / regulation of apoptotic process involved in outflow tract morphogenesis / substantia propria of cornea development / negative regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / ascending aorta morphogenesis / uterine wall breakdown / cardioblast differentiation / positive regulation of timing of catagen / positive regulation of cardioblast differentiation / cardiac right ventricle morphogenesis ...regulation of timing of catagen / regulation of apoptotic process involved in outflow tract morphogenesis / substantia propria of cornea development / negative regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / ascending aorta morphogenesis / uterine wall breakdown / cardioblast differentiation / positive regulation of timing of catagen / positive regulation of cardioblast differentiation / cardiac right ventricle morphogenesis / pharyngeal arch artery morphogenesis / type III transforming growth factor beta receptor binding / regulation of transforming growth factor beta2 production / atrial septum morphogenesis / positive regulation of heart contraction / positive regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / negative regulation of macrophage cytokine production / signaling / secondary palate development / positive regulation of stress-activated MAPK cascade / glial cell migration / somatic stem cell division / heart valve morphogenesis / endocardial cushion fusion / atrial septum primum morphogenesis / membranous septum morphogenesis / positive regulation of integrin biosynthetic process / cardiac epithelial to mesenchymal transition / eye development / cranial skeletal system development / neural retina development / embryonic digestive tract development / transforming growth factor beta receptor binding / type II transforming growth factor beta receptor binding / pulmonary valve morphogenesis / outflow tract septum morphogenesis / negative regulation of Ras protein signal transduction / ventricular trabecula myocardium morphogenesis / cell-cell junction organization / collagen fibril organization / positive regulation of cell adhesion mediated by integrin / embryonic limb morphogenesis / dopamine biosynthetic process / embryo development ending in birth or egg hatching / odontogenesis / Molecules associated with elastic fibres / atrioventricular valve morphogenesis / cardiac muscle cell proliferation / endocardial cushion morphogenesis / generation of neurons / hair follicle morphogenesis / ventricular septum morphogenesis / positive regulation of Notch signaling pathway / positive regulation of epithelial cell migration / activation of protein kinase activity / TGF-beta receptor signaling activates SMADs / inner ear development / uterus development / positive regulation of SMAD protein signal transduction / hemopoiesis / positive regulation of cell division / hair follicle development / ECM proteoglycans / neuron development / epithelial to mesenchymal transition / positive regulation of epithelial to mesenchymal transition / positive regulation of cell cycle / salivary gland morphogenesis / heart morphogenesis / extrinsic apoptotic signaling pathway / epithelial cell differentiation / negative regulation of angiogenesis / neutrophil chemotaxis / transforming growth factor beta receptor signaling pathway / platelet alpha granule lumen / response to progesterone / kidney development / skeletal system development / cytokine activity / neural tube closure / positive regulation of protein secretion / growth factor activity / wound healing / cell morphogenesis / negative regulation of cell growth / response to wounding / positive regulation of miRNA transcription / male gonad development / positive regulation of neuron apoptotic process / negative regulation of epithelial cell proliferation / positive regulation of immune response / cell migration / Platelet degranulation / regulation of cell population proliferation / heart development / amyloid-beta binding / positive regulation of cell growth / collagen-containing extracellular matrix / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / response to hypoxia Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.8 Å | ||||||
Authors | Daopin, S. / Davies, D.R. | ||||||
Citation | Journal: Science / Year: 1992 Title: Crystal structure of transforming growth factor-beta 2: an unusual fold for the superfamily. Authors: Daopin, S. / Piez, K.A. / Ogawa, Y. / Davies, D.R. #1: Journal: Proteins / Year: 1993 Title: Crystal Structure of Tgf-Beta2 Refined at 1.8 Angstroms Resolution Authors: Daopin, S. / Li, M. / Davies, D.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2tgi.cif.gz | 30.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2tgi.ent.gz | 23.3 KB | Display | PDB format |
PDBx/mmJSON format | 2tgi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tg/2tgi ftp://data.pdbj.org/pub/pdb/validation_reports/tg/2tgi | 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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Unit cell |
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Atom site foot note | 1: RESIDUE PRO 36 IS A CIS PROLINE. 2: RESIDUES 92 - 96 ARE ILL-DEFINED IN THE ELECTRON DENSITY. MAP. |
-Components
#1: Protein | Mass: 12732.597 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P61812 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.13 Å3/Da / Density % sol: 60.74 % | |||||||||||||||||||||||||
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Crystal grow | *PLUS Method: vapor diffusion | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 2.1 Å / Num. obs: 9706 / % possible obs: 87 % / Num. measured all: 54248 / Rmerge(I) obs: 0.047 |
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-Processing
Software | Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.8→8 Å / Rfactor obs: 0.173 | ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→8 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 15 Å / Rfactor obs: 0.172 / Rfactor Rwork: 0.172 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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