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Yorodumi- PDB-3crg: Crystal structure of human fibroblast growth factor-1 with mutati... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3crg | ||||||
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Title | Crystal structure of human fibroblast growth factor-1 with mutations Glu81Ala, Glu82Asn and Lys101Ala | ||||||
Components | Heparin-binding growth factor 1 | ||||||
Keywords | HORMONE / crystal packing / Angiogenesis / Developmental protein / Differentiation / Growth factor / Heparin-binding / Mitogen | ||||||
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 / Signaling by FGFR1 in disease / activation of protein kinase B activity / extracellular matrix / 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 / Negative regulation of FGFR1 signaling / animal organ morphogenesis / lung development / 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 | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Meher, A.K. / Honjo, E. / Kuroki, R. / Lee, J. / Somasundaram, T. / Blaber, M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2009 Title: Engineering an improved crystal contact across a solvent-mediated interface of human fibroblast growth factor 1. Authors: Meher, A.K. / Blaber, S.I. / Lee, J. / Honjo, E. / Kuroki, R. / Blaber, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3crg.cif.gz | 73.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3crg.ent.gz | 55.6 KB | Display | PDB format |
PDBx/mmJSON format | 3crg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cr/3crg ftp://data.pdbj.org/pub/pdb/validation_reports/cr/3crg | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 16555.600 Da / Num. of mol.: 2 / Mutation: E81A, E82N and K101A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FGF1, FGFA / Plasmid: pET21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: P05230 #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / | #5: 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: 2.98 Å3/Da / Density % sol: 58.67 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 3.1 M sodium formate and 0.4 M ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.541 Å |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Aug 20, 2007 |
Radiation | Monochromator: OSMIC MAX-FLUX CONFOCAL MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.541 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→20 Å / Num. obs: 30785 / % possible obs: 91.7 % / Redundancy: 6.6 % / Biso Wilson estimate: 16.3 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 1.85→1.89 Å / Redundancy: 4 % / Rmerge(I) obs: 0.198 / Mean I/σ(I) obs: 5.7 / % possible all: 54.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→19.96 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 386515.06 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 42.1138 Å2 / ksol: 0.388479 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.85→19.96 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.97 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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