+Open data
-Basic information
Entry | Database: PDB / ID: 1fq9 | ||||||||||||
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Title | CRYSTAL STRUCTURE OF A TERNARY FGF2-FGFR1-HEPARIN COMPLEX | ||||||||||||
Components |
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Keywords | GROWTH FACTOR/GROWTH FACTOR RECEPTOR / I-set subgroup within the immunoglobulin superfamily / b-trefoil fold / GROWTH FACTOR-GROWTH FACTOR RECEPTOR COMPLEX | ||||||||||||
Function / homology | Function and homology information growth factor dependent regulation of skeletal muscle satellite cell proliferation / positive regulation of inner ear auditory receptor cell differentiation / positive regulation of neuroepithelial cell differentiation / regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / positive regulation of lens fiber cell differentiation / positive regulation of endothelial cell chemotaxis to fibroblast growth factor / positive regulation of cell fate specification / regulation of retinal cell programmed cell death / Formation of intermediate mesoderm / regulation of cell migration involved in sprouting angiogenesis ...growth factor dependent regulation of skeletal muscle satellite cell proliferation / positive regulation of inner ear auditory receptor cell differentiation / positive regulation of neuroepithelial cell differentiation / regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / positive regulation of lens fiber cell differentiation / positive regulation of endothelial cell chemotaxis to fibroblast growth factor / positive regulation of cell fate specification / regulation of retinal cell programmed cell death / Formation of intermediate mesoderm / regulation of cell migration involved in sprouting angiogenesis / FGFRL1 modulation of FGFR1 signaling / corticotropin hormone secreting cell differentiation / thyroid-stimulating hormone-secreting cell differentiation / chondroblast differentiation / lymphatic endothelial cell migration / chemokine binding / negative regulation of fibroblast growth factor receptor signaling pathway / Signaling by FGFR1 amplification mutants / negative regulation of fibroblast growth factor production / positive regulation of mitotic cell cycle DNA replication / regulation of extrinsic apoptotic signaling pathway in absence of ligand / Signaling by plasma membrane FGFR1 fusions / diphosphate metabolic process / POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation / vitamin D3 metabolic process / FGFR1c and Klotho ligand binding and activation / regulation of phosphate transport / regulation of lateral mesodermal cell fate specification / positive regulation of cerebellar granule cell precursor proliferation / positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway / cementum mineralization / cerebellar granule cell precursor proliferation / positive regulation of stem cell differentiation / Formation of the nephric duct / response to sodium phosphate / positive regulation of epithelial tube formation / regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling / receptor-receptor interaction / regulation of endothelial cell chemotaxis to fibroblast growth factor / hyaluronan catabolic process / fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development / auditory receptor cell development / ventricular zone neuroblast division / Epithelial-Mesenchymal Transition (EMT) during gastrulation / inner ear auditory receptor cell differentiation / glial cell differentiation / negative regulation of wound healing / positive regulation of parathyroid hormone secretion / chordate embryonic development / stem cell development / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / Phospholipase C-mediated cascade; FGFR3 / mesenchymal cell proliferation / FGFR2b ligand binding and activation / embryonic morphogenesis / paraxial mesoderm development / fibroblast growth factor receptor binding / angiogenesis involved in coronary vascular morphogenesis / 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 / mammary gland epithelial cell differentiation / fibroblast growth factor receptor activity / Phospholipase C-mediated cascade; FGFR4 / branching involved in salivary gland morphogenesis / 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 phospholipase activity / lung-associated mesenchyme development / paracrine signaling / cell projection assembly / negative regulation of fibroblast migration / cellular response to fibroblast growth factor stimulus / cell migration involved in sprouting angiogenesis / outer ear morphogenesis / middle ear morphogenesis / negative regulation of blood vessel endothelial cell migration / embryonic limb morphogenesis / embryo development ending in birth or egg hatching / skeletal system morphogenesis / endothelial cell proliferation / positive regulation of vascular endothelial cell proliferation / cardiac muscle cell proliferation / positive regulation of mesenchymal cell proliferation / positive regulation of endothelial cell chemotaxis / ureteric bud development / Signaling by FGFR2 IIIa TM / inner ear morphogenesis / midbrain development / Syndecan interactions / branching involved in ureteric bud morphogenesis / positive regulation of cell migration involved in sprouting angiogenesis / positive regulation of DNA biosynthetic process / PI-3K cascade:FGFR3 Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å | ||||||||||||
Authors | Schlessinger, J. / Plotnikov, A.N. / Ibrahimi, O.A. / Eliseenkova, A.V. / Yeh, B.K. / Yayon, A. / Linhardt, R.J. / Mohammadi, M. | ||||||||||||
Citation | Journal: Mol.Cell / Year: 2000 Title: Crystal structure of a ternary FGF-FGFR-heparin complex reveals a dual role for heparin in FGFR binding and dimerization. Authors: Schlessinger, J. / Plotnikov, A.N. / Ibrahimi, O.A. / Eliseenkova, A.V. / Yeh, B.K. / Yayon, A. / Linhardt, R.J. / Mohammadi, M. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fq9.cif.gz | 143 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fq9.ent.gz | 118.9 KB | Display | PDB format |
PDBx/mmJSON format | 1fq9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fq9_validation.pdf.gz | 554.4 KB | Display | wwPDB validaton report |
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Full document | 1fq9_full_validation.pdf.gz | 590.8 KB | Display | |
Data in XML | 1fq9_validation.xml.gz | 20 KB | Display | |
Data in CIF | 1fq9_validation.cif.gz | 29.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fq/1fq9 ftp://data.pdbj.org/pub/pdb/validation_reports/fq/1fq9 | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 15110.339 Da / Num. of mol.: 2 Fragment: THE B-TREFOIL CORE OF FIBROBLAST GROWTH FACTOR 2 (FGF2) Mutation: C69S, C87S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P09038 #2: Protein | Mass: 25274.805 Da / Num. of mol.: 2 Fragment: EXTRACELLULAR LIGAND BINDING DOMAIN OF FGF RECEPTOR 1 (FGFR1) CONSISTING OF IMMUNOGLOBULIN LIKE DOMAINS II (D2) AND III (D3) Mutation: N185Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P11362 #3: Polysaccharide | 4-deoxy-2-O-sulfo-alpha-L-threo-hex-4-enopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)- ...4-deoxy-2-O-sulfo-alpha-L-threo-hex-4-enopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-beta-L-altropyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose | Type: oligosaccharide / Mass: 2309.882 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source #4: Polysaccharide | 4-deoxy-2-O-sulfo-alpha-L-threo-hex-4-enopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)- ...4-deoxy-2-O-sulfo-alpha-L-threo-hex-4-enopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose | Source method: isolated from a genetically manipulated source |
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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: 2.97 Å3/Da / Density % sol: 58.57 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: Ammonium sulfate, Glycerol, Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K | ||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 58 % | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9788 |
Detector | Type: SDMS / Detector: AREA DETECTOR / Date: Jun 22, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9788 Å / Relative weight: 1 |
Reflection | Resolution: 3→30 Å / Num. all: 97669 / Num. obs: 97669 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.94 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 3→3.11 Å / Rmerge(I) obs: 0.303 / % possible all: 92.6 |
Reflection | *PLUS Num. obs: 19774 / Num. measured all: 97669 |
Reflection shell | *PLUS % possible obs: 92.6 % |
-Processing
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Refinement | Resolution: 3→25 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 3→25 Å
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Refine LS restraints |
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