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Yorodumi- PDB-1bfc: BASIC FIBROBLAST GROWTH FACTOR COMPLEXED WITH HEPARIN HEXAMER FRAGMENT -
+Open data
-Basic information
Entry | Database: PDB / ID: 1bfc | |||||||||
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Title | BASIC FIBROBLAST GROWTH FACTOR COMPLEXED WITH HEPARIN HEXAMER FRAGMENT | |||||||||
Components | BASIC FIBROBLAST GROWTH FACTOR | |||||||||
Keywords | GROWTH FACTOR / MITOGEN / VASCULARIZATION / HEPARIN-BINDING | |||||||||
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 endothelial cell chemotaxis to fibroblast growth factor / 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 ...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 endothelial cell chemotaxis to fibroblast growth factor / 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 / cerebellar granule cell precursor proliferation / positive regulation of stem cell differentiation / Formation of the nephric duct / positive regulation of epithelial tube formation / receptor-receptor interaction / regulation of endothelial cell chemotaxis to fibroblast growth factor / hyaluronan catabolic process / inner ear auditory receptor cell differentiation / glial 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 / FGFR2b ligand binding and activation / embryonic morphogenesis / fibroblast growth factor receptor binding / angiogenesis involved in coronary vascular morphogenesis / FGFR2c ligand binding and activation / Activated point mutants of FGFR2 / 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 / cell migration involved in sprouting angiogenesis / negative regulation of blood vessel endothelial cell migration / embryo development ending in birth or egg hatching / endothelial cell proliferation / positive regulation of vascular endothelial cell proliferation / positive regulation of endothelial cell chemotaxis / Signaling by FGFR2 IIIa TM / Syndecan interactions / branching involved in ureteric bud morphogenesis / positive regulation of cell migration involved in sprouting angiogenesis / positive regulation of DNA biosynthetic process / PI-3K cascade:FGFR3 / positive regulation of neuroblast proliferation / PI-3K cascade:FGFR2 / positive regulation of stem cell proliferation / PI-3K cascade:FGFR4 / positive regulation of sprouting angiogenesis / chemoattractant activity / PI-3K cascade:FGFR1 / positive regulation of cell division / Non-integrin membrane-ECM interactions / PI3K Cascade / neuroblast proliferation / response to axon injury / canonical Wnt signaling pathway / positive regulation of blood vessel endothelial cell migration / fibroblast growth factor receptor signaling pathway / regulation of angiogenesis / positive regulation of osteoblast differentiation / SHC-mediated cascade:FGFR3 / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / SHC-mediated cascade:FGFR1 / negative regulation of stem cell proliferation / FRS-mediated FGFR3 signaling / release of sequestered calcium ion into cytosol / positive regulation of cardiac muscle cell proliferation / FRS-mediated FGFR2 signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR4 signaling / FRS-mediated FGFR1 signaling / positive regulation of vascular associated smooth muscle cell proliferation / Signaling by FGFR2 in disease / positive regulation of endothelial cell proliferation / substantia nigra development / ERK1 and ERK2 cascade / Signaling by FGFR1 in disease / regulation of cell migration / phosphatidylinositol 3-kinase/protein kinase B signal transduction Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 2.2 Å | |||||||||
Authors | Faham, S. / Rees, D.C. | |||||||||
Citation | Journal: Science / Year: 1996 Title: Heparin structure and interactions with basic fibroblast growth factor. Authors: Faham, S. / Hileman, R.E. / Fromm, J.R. / Linhardt, R.J. / Rees, D.C. #1: Journal: Science / Year: 1991 Title: Three-Dimensional Structures of Acidic and Basic Fibroblast Growth Factors Authors: Zhu, X. / Komiya, H. / Chirino, A. / Faham, S. / Fox, G.M. / Arakawa, T. / Hsu, B.T. / Rees, D.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bfc.cif.gz | 42.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bfc.ent.gz | 28.8 KB | Display | PDB format |
PDBx/mmJSON format | 1bfc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1bfc_validation.pdf.gz | 466.7 KB | Display | wwPDB validaton report |
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Full document | 1bfc_full_validation.pdf.gz | 480 KB | Display | |
Data in XML | 1bfc_validation.xml.gz | 6.5 KB | Display | |
Data in CIF | 1bfc_validation.cif.gz | 8.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bf/1bfc ftp://data.pdbj.org/pub/pdb/validation_reports/bf/1bfc | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 16516.883 Da / Num. of mol.: 1 / Mutation: C70S, C88S / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P09038 |
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#2: Polysaccharide | 4-deoxy-2-O-sulfo-alpha-L-threo-hex-4-enopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)- ...4-deoxy-2-O-sulfo-alpha-L-threo-hex-4-enopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose Source method: isolated from a genetically manipulated source |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.8 Å3/Da / Density % sol: 31.69 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 7 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.54 |
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Detector | Detector: AREA DETECTOR |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→40 Å / Num. obs: 6123 / % possible obs: 94.7 % |
Reflection | *PLUS Rmerge(I) obs: 0.073 |
-Processing
Software |
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Refinement | Resolution: 2.2→6 Å / σ(F): 1
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Refinement step | Cycle: LAST / Resolution: 2.2→6 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |