+Open data
-Basic information
Entry | Database: PDB / ID: 3ud7 | |||||||||
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Title | Crystal Structure Analysis of FGF1-Disaccharide(NI21) complexes | |||||||||
Components | Heparin-binding growth factor 1 | |||||||||
Keywords | HORMONE / Heparin/Heparan sulfate Binding | |||||||||
Function / homology | Function and homology information mesonephric epithelium development / branch elongation involved in ureteric bud branching / regulation of endothelial tube morphogenesis / FGFR3b ligand binding and activation / regulation of endothelial cell chemotaxis to fibroblast growth factor / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / Phospholipase C-mediated cascade; FGFR3 / FGFR2b ligand binding and activation / positive regulation of cholesterol biosynthetic process ...mesonephric epithelium development / branch elongation involved in ureteric bud branching / regulation of endothelial tube morphogenesis / FGFR3b ligand binding and activation / regulation of endothelial cell chemotaxis to fibroblast growth factor / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / Phospholipase C-mediated cascade; FGFR3 / FGFR2b ligand binding and activation / positive regulation of cholesterol biosynthetic process / fibroblast growth factor receptor binding / 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 / 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 / positive regulation of hepatocyte proliferation / S100 protein binding / positive regulation of intracellular signal transduction / Signaling by FGFR2 IIIa TM / PI-3K cascade:FGFR3 / PI-3K cascade:FGFR2 / positive regulation of sprouting angiogenesis / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / positive regulation of cell division / PI3K Cascade / fibroblast growth factor receptor signaling pathway / anatomical structure morphogenesis / SHC-mediated cascade:FGFR3 / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / SHC-mediated cascade:FGFR1 / FRS-mediated FGFR3 signaling / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR1 signaling / Signaling by FGFR2 in disease / Hsp70 protein binding / Signaling by FGFR1 in disease / activation of protein kinase B activity / positive regulation of endothelial cell migration / extracellular matrix / epithelial cell proliferation / positive regulation of epithelial cell proliferation / Negative regulation of FGFR3 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / animal organ morphogenesis / Negative regulation of FGFR1 signaling / growth factor activity / positive regulation of MAP kinase activity / lung development / wound healing / positive regulation of angiogenesis / Constitutive Signaling by Aberrant PI3K in Cancer / integrin binding / PIP3 activates AKT signaling / heparin binding / cellular response to heat / cell cortex / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / angiogenesis / positive regulation of ERK1 and ERK2 cascade / cell differentiation / positive regulation of cell migration / positive regulation of cell population proliferation / positive regulation of gene expression / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / nucleoplasm / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | |||||||||
Authors | Hung, S.-C. / Shi, Z. | |||||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2012 Title: Divergent synthesis of 48 heparan sulfate-based disaccharides and probing the specific sugar-fibroblast growth factor-1 interaction Authors: Hu, Y.-P. / Zhong, Y.-Q. / Chen, Z.-G. / Chen, C.-Y. / Shi, Z. / Zulueta, M.M.L. / Ku, C.-C. / Lee, P.-Y. / Wang, C.-C. / Hung, S.-C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ud7.cif.gz | 165.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ud7.ent.gz | 131.1 KB | Display | PDB format |
PDBx/mmJSON format | 3ud7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ud7_validation.pdf.gz | 865.9 KB | Display | wwPDB validaton report |
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Full document | 3ud7_full_validation.pdf.gz | 874.6 KB | Display | |
Data in XML | 3ud7_validation.xml.gz | 17.3 KB | Display | |
Data in CIF | 3ud7_validation.cif.gz | 22.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ud/3ud7 ftp://data.pdbj.org/pub/pdb/validation_reports/ud/3ud7 | HTTPS FTP |
-Related structure data
Related structure data | 3ud8C 3ud9C 3udaC 1rg8S 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 15989.062 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FGF1 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P05230 #2: Polysaccharide | 2-deoxy-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: Chemical | ChemComp-PO4 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.04 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 2M (NH4)HPO4, 0.1M sodium acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 29, 2011 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→80.67 Å / Num. all: 10833 / Num. obs: 10803 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 5 / Redundancy: 3.6 % / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 2 / Num. unique all: 1059 / Rsym value: 0.438 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RG8 Resolution: 2.8→80.67 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.901 / SU B: 35.705 / SU ML: 0.322 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.44 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.131 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→80.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.799→2.872 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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