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Yorodumi- PDB-2erm: Solution structure of a biologically active human FGF-1 monomer, ... -
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-Basic information
Entry | Database: PDB / ID: 2erm | |||||||||
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Title | Solution structure of a biologically active human FGF-1 monomer, complexed to a hexasaccharide heparin-analogue | |||||||||
Components | Heparin-binding growth factor 1 | |||||||||
Keywords | HORMONE/GROWTH FACTOR / HEPARIN-LIKE HEXASACCHARIDE / FIBROBLAST GROWTH FACTOR / PROTEIN-CARBOHYDRATE COMPLEX / HORMONE-GROWTH FACTOR COMPLEX | |||||||||
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 / positive regulation of sprouting angiogenesis / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / positive regulation of cell division / PI3K Cascade / anatomical structure morphogenesis / fibroblast growth factor receptor signaling pathway / 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 / Hsp70 protein binding / Signaling by FGFR2 in disease / extracellular matrix / Signaling by FGFR1 in disease / activation of protein kinase B activity / positive regulation of endothelial cell migration / epithelial cell proliferation / positive regulation of epithelial cell proliferation / Negative regulation of FGFR3 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / lung development / Negative regulation of FGFR1 signaling / animal organ morphogenesis / growth factor activity / positive regulation of MAP kinase activity / wound healing / positive regulation of angiogenesis / Constitutive Signaling by Aberrant PI3K in Cancer / integrin binding / PIP3 activates AKT signaling / cellular response to heat / heparin binding / cell cortex / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / angiogenesis / cell differentiation / positive regulation of ERK1 and ERK2 cascade / 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 / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | SOLUTION NMR / Simulated annealing, restrained molecular dynamics | |||||||||
Authors | Canales, A. / Lozano, R. / Nieto, P.M. / Martin-Lomas, M. / Gimenez-Gallego, G. / Jimenez-Barbero, J. | |||||||||
Citation | Journal: Febs J. / Year: 2006 Title: Solution NMR structure of a human FGF-1 monomer, activated by a hexasaccharide heparin-analogue. Authors: Canales, A. / Lozano, R. / Lopez-Mendez, B. / Angulo, J. / Ojeda, R. / Nieto, P.M. / Martin-Lomas, M. / Gimenez-Gallego, G. / Jimenez-Barbero, J. #1: Journal: Biochemistry / Year: 2000 Title: 1H NMR structural characterization of a nonmitogenic, vasodilatory, ischemia-protector and neuromodulatory acidic fibroblast growth factor Authors: Lozano, R.M. / Pineda-Lucena, A. / Gonzalez, C. / Jimenez, M.A. / Cuevas, P. / Redondo-Horcajo, M. / Sanz, J.M. / Rico, M. / Gimenez-Gallego, G. #2: Journal: J.Biol.Chem. / Year: 2003 Title: Leads for development of new naphthalenesulfonate derivatives with enhanced antiangiogenic activity: crystal structure of acidic fibroblast growth factor in complex with 5-amino-2-naphthalene sulfonate Authors: Fernandez-Tornero, C. / Lozano, R.M. / Redondo-Horcajo, M. / Gomez, A. / Lopez, J. / Uriel, C. / Valverde, S. / Cuevas, P. / Romero, A. / Gimenez-Gallego, G. #3: Journal: Proteins / Year: 2004 Title: An atomic resolution structure for human fibroblast growth factor 1 Authors: Bernett, M.J. / Somasundaram, T. / Blaber, M. #4: Journal: Nature / Year: 1998 Title: Structure of a heparin-linked biologically active dimer of fibroblast growth factor Authors: DiGabriele, A.D. / Lax, I. / Chen, D.I. / Svahn, C.M. / Jaye, M. / Schlessinger, J. / Hendrickson, W.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2erm.cif.gz | 880.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2erm.ent.gz | 738.7 KB | Display | PDB format |
PDBx/mmJSON format | 2erm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/er/2erm ftp://data.pdbj.org/pub/pdb/validation_reports/er/2erm | 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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NMR ensembles |
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-Components
#1: Protein | Mass: 15710.691 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FGF1, FGFA / Plasmid: pRAT4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P05230 |
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#2: Polysaccharide | 2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2- ...2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-acetamido-2-deoxy-6-O-sulfo-alpha-D-glucopyranose-(1-4)-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid Source method: isolated from a genetically manipulated source |
#3: Chemical | ChemComp-IPA / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample conditions | Ionic strength: 150 mM NaCl / pH: 6.0 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
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Radiation wavelength | Relative weight: 1 | |||||||||||||||
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: Simulated annealing, restrained molecular dynamics / Software ordinal: 1 Details: The first six residues of the protein could not be assigned due to the disorder of the N-terminus region. These are shown as missing residues in remark 465 in all the models. The anomalous ...Details: The first six residues of the protein could not be assigned due to the disorder of the N-terminus region. These are shown as missing residues in remark 465 in all the models. The anomalous torsion angles observed for his 107 and glu 105 are also found in the related pdbs 1dzd and 1dzc of fgf-1. Most of the peptide bonds that deviate significantly from both cis and trans conformation, shown in remark 500, correspond to residues implicated in the binding of the ligand. | ||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 30 / Conformers submitted total number: 20 |