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Yorodumi- PDB-1jt7: Human Acidic Fibroblast Growth Factor. 141 Amino Acid Form with A... -
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-Basic information
Entry | Database: PDB / ID: 1jt7 | ||||||
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Title | Human Acidic Fibroblast Growth Factor. 141 Amino Acid Form with Amino Terminal His Tag AND LEU 44 REPLACED BY PHE AND LEU 73 REPLACED BY VAL AND VAL 109 REPLACED BY LEU (L44F/L73V/V109L) | ||||||
Components | acidic fibroblast growth factor | ||||||
Keywords | HORMONE/GROWTH FACTOR / beta-trefoil / 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 / 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 / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Brych, S.R. / Blaber, S.I. / Logan, T.M. / Blaber, M. | ||||||
Citation | Journal: Protein Sci. / Year: 2001 Title: Structure and stability effects of mutations designed to increase the primary sequence symmetry within the core region of a beta-trefoil. Authors: Brych, S.R. / Blaber, S.I. / Logan, T.M. / Blaber, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jt7.cif.gz | 134.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jt7.ent.gz | 103.8 KB | Display | PDB format |
PDBx/mmJSON format | 1jt7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jt7_validation.pdf.gz | 432.2 KB | Display | wwPDB validaton report |
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Full document | 1jt7_full_validation.pdf.gz | 444.4 KB | Display | |
Data in XML | 1jt7_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | 1jt7_validation.cif.gz | 23.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jt/1jt7 ftp://data.pdbj.org/pub/pdb/validation_reports/jt/1jt7 | HTTPS FTP |
-Related structure data
Related structure data | 1jqzSC 1jt3C 1jt4C 1jt5C 1jtcC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 16720.764 Da / Num. of mol.: 4 / Mutation: L44F,L73V,V109L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P05230 #2: Chemical | ChemComp-SO4 / #3: Chemical | #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: 2.95 Å3/Da / Density % sol: 57.66 % | ||||||||||||||||||||
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: sodium formate, ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K | ||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 or 10 ℃ | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Feb 22, 2001 / Details: Osmic Blue confocal mirrors |
Radiation | Monochromator: Osmic Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30.9 Å / Num. all: 85399 / Num. obs: 85399 / % possible obs: 87.6 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 2.9 % / Biso Wilson estimate: 14.1 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 31.5 |
Reflection shell | Resolution: 1.7→1.74 Å / Rmerge(I) obs: 0.311 / Mean I/σ(I) obs: 3.1 / % possible all: 47.1 |
Reflection | *PLUS Num. obs: 71811 / Num. measured all: 455187 |
Reflection shell | *PLUS % possible obs: 78.1 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1JQZ Resolution: 1.7→30.9 Å / Isotropic thermal model: TRONRUD / Stereochemistry target values: TRONRUD
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Solvent computation | Solvent model: TNT / Bsol: 187.39 Å2 / ksol: 0.857 e/Å3 | ||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→30.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.73 Å /
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Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||||||
Refinement | *PLUS Num. reflection Rfree: 7105 / % reflection Rfree: 10 % / Rfactor all: 0.196 / Rfactor obs: 0.192 / Rfactor Rfree: 0.234 / Rfactor Rwork: 0.192 | ||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||
Refine LS restraints | *PLUS
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