+Open data
-Basic information
Entry | Database: PDB / ID: 4oef | |||||||||
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Title | Crystal Structure Analysis of FGF2-Disaccharide (S6I2) complex | |||||||||
Components | Fibroblast growth factor 2 | |||||||||
Keywords | PROTEIN BINDING / Heparin/Heparin Sulfate 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 / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Li, Y.C. / Hsiao, C.D. | |||||||||
Citation | Journal: Acs Chem.Biol. / Year: 2014 Title: Interactions that influence the binding of synthetic heparan sulfate based disaccharides to fibroblast growth factor-2. Authors: Li, Y.C. / Ho, I.H. / Ku, C.C. / Zhong, Y.Q. / Hu, Y.P. / Chen, Z.G. / Chen, C.Y. / Lin, W.C. / Zulueta, M.M. / Hung, S.C. / Lin, M.G. / Wang, C.C. / Hsiao, C.D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4oef.cif.gz | 43.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4oef.ent.gz | 27.7 KB | Display | PDB format |
PDBx/mmJSON format | 4oef.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4oef_validation.pdf.gz | 834.6 KB | Display | wwPDB validaton report |
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Full document | 4oef_full_validation.pdf.gz | 834.7 KB | Display | |
Data in XML | 4oef_validation.xml.gz | 8.4 KB | Display | |
Data in CIF | 4oef_validation.cif.gz | 10.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oe/4oef ftp://data.pdbj.org/pub/pdb/validation_reports/oe/4oef | HTTPS FTP |
-Related structure data
Related structure data | 4oeeC 4oegC 1bfcS C: citing same article (ref.) S: Starting model for refinement |
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Similar 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: 17249.732 Da / Num. of mol.: 1 / Mutation: C69S, C87S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FGF2, FGFB / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(RIPL) / References: UniProt: P09038 |
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#2: Polysaccharide | 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-1-O-methyl-2-O-sulfo-alpha-L-idopyranuronic acid Source method: isolated from a genetically manipulated source |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.79 Å3/Da / Density % sol: 31.41 % |
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Crystal grow | Temperature: 299 K / Method: vapor diffusion, hanging drop / pH: 4.2 Details: 40% polyethylene glycol 600 and 100 mM Na2HPO4/citric acid, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 299K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: May 22, 2012 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→25 Å / Num. all: 10466 / Num. obs: 10466 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 5 / Redundancy: 3.9 % / Rmerge(I) obs: 0.046 / Rsym value: 0.046 / Net I/σ(I): 36.2 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.274 / Mean I/σ(I) obs: 6.7 / Rsym value: 0.274 / % possible all: 91 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BFC Resolution: 1.8→24.304 Å / SU ML: 0.17 / σ(F): 1.97 / Phase error: 25.12 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→24.304 Å
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Refine LS restraints |
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LS refinement shell |
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