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Yorodumi- PDB-1qqk: THE CRYSTAL STRUCTURE OF FIBROBLAST GROWTH FACTOR 7 (KERATINOCYTE... -
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-Basic information
Entry | Database: PDB / ID: 1qqk | ||||||
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Title | THE CRYSTAL STRUCTURE OF FIBROBLAST GROWTH FACTOR 7 (KERATINOCYTE GROWTH FACTOR) | ||||||
Components | FIBROBLAST GROWTH FACTOR 7 | ||||||
Keywords | HORMONE/GROWTH FACTOR / BETA-TREFOIL / HORMONE-GROWTH FACTOR COMPLEX | ||||||
Function / homology | Function and homology information secretion by lung epithelial cell involved in lung growth / FGFR2b ligand binding and activation / type 2 fibroblast growth factor receptor binding / SHC-mediated cascade:FGFR2 / FRS-mediated FGFR2 signaling / PI-3K cascade:FGFR2 / PI3K Cascade / Phospholipase C-mediated cascade; FGFR2 / PIP3 activates AKT signaling / positive regulation of epithelial cell proliferation involved in lung morphogenesis ...secretion by lung epithelial cell involved in lung growth / FGFR2b ligand binding and activation / type 2 fibroblast growth factor receptor binding / SHC-mediated cascade:FGFR2 / FRS-mediated FGFR2 signaling / PI-3K cascade:FGFR2 / PI3K Cascade / Phospholipase C-mediated cascade; FGFR2 / PIP3 activates AKT signaling / positive regulation of epithelial cell proliferation involved in lung morphogenesis / positive regulation of keratinocyte proliferation / Negative regulation of FGFR2 signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling / positive regulation of myoblast proliferation / phosphatidylcholine biosynthetic process / phospholipid biosynthetic process / branching involved in salivary gland morphogenesis / positive regulation of keratinocyte migration / mesenchymal cell proliferation / regulation of synapse maturation / surfactant homeostasis / protein localization to cell surface / RAF/MAP kinase cascade / myoblast proliferation / endothelial cell proliferation / hair follicle morphogenesis / positive chemotaxis / chemoattractant activity / positive regulation of cell division / fibroblast growth factor receptor signaling pathway / ovarian follicle development / GABA-ergic synapse / positive regulation of endothelial cell proliferation / regulation of cell migration / positive regulation of epithelial cell proliferation / epithelial cell proliferation / animal organ morphogenesis / lung development / growth factor activity / positive regulation of peptidyl-tyrosine phosphorylation / heparin binding / actin cytoskeleton organization / postsynapse / positive regulation of MAPK cascade / cell differentiation / positive regulation of cell population proliferation / positive regulation of gene expression / positive regulation of DNA-templated transcription / Golgi apparatus / extracellular space / extracellular region / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.1 Å | ||||||
Authors | Ye, S. / Luo, Y. / Pelletier, H. / McKeehan, W.L. | ||||||
Citation | Journal: Biochemistry / Year: 2001 Title: Structural basis for interaction of FGF-1, FGF-2, and FGF-7 with different heparan sulfate motifs. Authors: Ye, S. / Luo, Y. / Lu, W. / Jones, R.B. / Linhardt, R.J. / Capila, I. / Toida, T. / Kan, M. / Pelletier, H. / McKeehan, W.L. #1: Journal: Biochemistry / Year: 1998 Title: The glycine box: a determinant of specificity for fibroblast growth factor Authors: Luo, Y. / Lu, W. / Mohamedali, K.A. / Jang, J.H. / Jones, R.B. / Gabriel, J.L. / Kan, M. / McKeehan, W.L. #2: Journal: Science / Year: 1989 Title: Human KGF is FGF-related with properties of a paracrine effector of epithelial cell growth. Authors: Finch, P.W. / Rubin, J.S. / Miki, T. / Ron, D. / Aaronson, S.A. #3: 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. #4: Journal: Science / Year: 1996 Title: Heparin structure and interactions with basic fibroblast growth factor. Authors: Faham, S. / Hileman, R.E. / Fromm, J.R. / Linhardt, R.J. / Rees, D.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qqk.cif.gz | 65.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qqk.ent.gz | 49.4 KB | Display | PDB format |
PDBx/mmJSON format | 1qqk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qqk_validation.pdf.gz | 422.8 KB | Display | wwPDB validaton report |
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Full document | 1qqk_full_validation.pdf.gz | 441.1 KB | Display | |
Data in XML | 1qqk_validation.xml.gz | 15.5 KB | Display | |
Data in CIF | 1qqk_validation.cif.gz | 20.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qq/1qqk ftp://data.pdbj.org/pub/pdb/validation_reports/qq/1qqk | HTTPS FTP |
-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
#1: Protein | Mass: 16269.858 Da / Num. of mol.: 2 / Fragment: FGF-7BETA (SER-54) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Organ: PROSTATE / Plasmid: PGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q02195 #2: 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: 3.44 Å3/Da / Density % sol: 64.22 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5 Details: SODIUM PHOSPHATE, POTASSIUM PHOSPHATE, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 99 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9296 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9296 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→30 Å / Num. all: 8036 / Num. obs: 8036 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Rmerge(I) obs: 0.129 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 3.1→3.21 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.447 / % possible all: 81.6 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. measured all: 48247 |
Reflection shell | *PLUS % possible obs: 81.6 % |
-Processing
Software |
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Refinement | Resolution: 3.1→10 Å / σ(F): 2 / σ(I): 2
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Refinement step | Cycle: LAST / Resolution: 3.1→10 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.843 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 3.1 Å / Lowest resolution: 10 Å / σ(F): 2 / Rfactor obs: 0.233 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |