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Yorodumi- PDB-4fgf: REFINEMENT OF THE STRUCTURE OF HUMAN BASIC FIBROBLAST GROWTH FACT... -
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-Basic information
Entry | Database: PDB / ID: 4fgf | |||||||||
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Title | REFINEMENT OF THE STRUCTURE OF HUMAN BASIC FIBROBLAST GROWTH FACTOR AT 1.6 ANGSTROMS RESOLUTION AND ANALYSIS OF PRESUMED HEPARIN BINDING SITES BY SELENATE SUBSTITUTION | |||||||||
Components | BASIC FIBROBLAST GROWTH FACTOR | |||||||||
Keywords | GROWTH FACTOR | |||||||||
Function / homology | Function and homology information growth factor dependent regulation of skeletal muscle satellite cell proliferation / positive regulation of inner ear auditory receptor cell differentiation / positive regulation of neuroepithelial cell differentiation / regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / positive regulation of lens fiber cell differentiation / positive regulation of cell fate specification / regulation of retinal cell programmed cell death / Formation of intermediate mesoderm / regulation of cell migration involved in sprouting angiogenesis / FGFRL1 modulation of FGFR1 signaling ...growth factor dependent regulation of skeletal muscle satellite cell proliferation / positive regulation of inner ear auditory receptor cell differentiation / positive regulation of neuroepithelial cell differentiation / regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / positive regulation of lens fiber cell differentiation / positive regulation of cell fate specification / regulation of retinal cell programmed cell death / Formation of intermediate mesoderm / regulation of cell migration involved in sprouting angiogenesis / FGFRL1 modulation of FGFR1 signaling / corticotropin hormone secreting cell differentiation / thyroid-stimulating hormone-secreting cell differentiation / chondroblast differentiation / lymphatic endothelial cell migration / chemokine binding / negative regulation of fibroblast growth factor receptor signaling pathway / POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation / positive regulation of cerebellar granule cell precursor proliferation / positive regulation of endothelial cell chemotaxis to fibroblast growth factor / cerebellar granule cell precursor proliferation / receptor-receptor interaction / positive regulation of stem cell differentiation / hyaluronan catabolic process / glial cell differentiation / regulation of endothelial cell chemotaxis to fibroblast growth factor / inner ear auditory receptor cell differentiation / negative regulation of wound healing / stem cell development / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / Phospholipase C-mediated cascade; FGFR3 / embryonic morphogenesis / FGFR2b ligand binding and activation / fibroblast growth factor receptor binding / angiogenesis involved in coronary vascular morphogenesis / FGFR2c ligand binding and activation / Activated point mutants of FGFR2 / positive regulation of epithelial tube formation / Phospholipase C-mediated cascade; FGFR2 / FGFR4 ligand binding and activation / FGFR1b ligand binding and activation / mammary gland epithelial cell differentiation / Phospholipase C-mediated cascade; FGFR4 / Signaling by activated point mutants of FGFR1 / FGFR1c ligand binding and activation / organ induction / Downstream signaling of activated FGFR1 / Phospholipase C-mediated cascade: FGFR1 / paracrine signaling / negative regulation of fibroblast migration / positive regulation of endothelial cell chemotaxis / endothelial cell proliferation / cell migration involved in sprouting angiogenesis / embryo development ending in birth or egg hatching / positive regulation of vascular endothelial cell proliferation / Signaling by FGFR2 IIIa TM / positive regulation of DNA biosynthetic process / Syndecan interactions / branching involved in ureteric bud morphogenesis / positive regulation of neuroblast proliferation / positive regulation of cell migration involved in sprouting angiogenesis / PI-3K cascade:FGFR3 / positive regulation of stem cell proliferation / positive regulation of sprouting angiogenesis / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / chemoattractant activity / negative regulation of blood vessel endothelial cell migration / positive regulation of cell division / Non-integrin membrane-ECM interactions / neuroblast proliferation / PI3K Cascade / canonical Wnt signaling pathway / response to axon injury / positive regulation of blood vessel endothelial cell migration / fibroblast growth factor receptor signaling pathway / positive regulation of osteoblast differentiation / regulation of angiogenesis / SHC-mediated cascade:FGFR3 / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / SHC-mediated cascade:FGFR1 / negative regulation of stem cell proliferation / release of sequestered calcium ion into cytosol / FRS-mediated FGFR3 signaling / FRS-mediated FGFR2 signaling / positive regulation of cardiac muscle cell proliferation / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR1 signaling / ERK1 and ERK2 cascade / positive regulation of vascular associated smooth muscle cell proliferation / Signaling by FGFR2 in disease / substantia nigra development / Signaling by FGFR1 in disease / positive regulation of endothelial cell proliferation / positive regulation of endothelial cell migration / nuclear receptor coactivator activity / phosphatidylinositol 3-kinase/protein kinase B signal transduction Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 1.6 Å | |||||||||
Authors | Eriksson, A.E. / Matthews, B.W. | |||||||||
Citation | Journal: Protein Sci. / Year: 1993 Title: Refinement of the structure of human basic fibroblast growth factor at 1.6 A resolution and analysis of presumed heparin binding sites by selenate substitution. Authors: Eriksson, A.E. / Cousens, L.S. / Matthews, B.W. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1991 Title: Three-Dimensional Structure of Human Basic Fibroblast Growth Factor Authors: Eriksson, A.E. / Cousens, L.S. / Weaver, L.H. / Matthews, B.W. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4fgf.cif.gz | 34.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fgf.ent.gz | 26.9 KB | Display | PDB format |
PDBx/mmJSON format | 4fgf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fg/4fgf ftp://data.pdbj.org/pub/pdb/validation_reports/fg/4fgf | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: SG SEO 69 IS BONDED TO SG CYS 69 AND SG SEO 92 IS BONDED TO SD CYS 92. |
-Components
#1: Protein | Mass: 16435.857 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P09038 | ||
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#2: Chemical | ChemComp-SO4 / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.83 Å3/Da / Density % sol: 32.96 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 8.1 / Method: vapor diffusion / Details: using macroseeding | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
-Processing
Software | Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.6→20 Å / Rfactor obs: 0.161 | ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→20 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 1.6 Å / Lowest resolution: 20 Å / Rfactor obs: 0.161 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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