+Open data
-Basic information
Entry | Database: PDB / ID: 1e0o | |||||||||
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Title | CRYSTAL STRUCTURE OF A TERNARY FGF1-FGFR2-HEPARIN COMPLEX | |||||||||
Components | (FIBROBLAST GROWTH FACTOR ...) x 2 | |||||||||
Keywords | GROWTH FACTOR / RECEPTOR TYROSINE KINASE / HEPARIN / TERNARY COMPLEX / SIGNAL TRANSDUCTION | |||||||||
Function / homology | Function and homology information Signaling by FGFR2 amplification mutants / Signaling by FGFR2 fusions / fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptotic process in bone marrow cell / fibroblast growth factor receptor signaling pathway involved in hemopoiesis / fibroblast growth factor receptor signaling pathway involved in positive regulation of cell proliferation in bone marrow / fibroblast growth factor receptor signaling pathway involved in mammary gland specification / lateral sprouting from an epithelium / mammary gland bud formation / branch elongation involved in salivary gland morphogenesis / mesenchymal cell differentiation involved in lung development ...Signaling by FGFR2 amplification mutants / Signaling by FGFR2 fusions / fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptotic process in bone marrow cell / fibroblast growth factor receptor signaling pathway involved in hemopoiesis / fibroblast growth factor receptor signaling pathway involved in positive regulation of cell proliferation in bone marrow / fibroblast growth factor receptor signaling pathway involved in mammary gland specification / lateral sprouting from an epithelium / mammary gland bud formation / branch elongation involved in salivary gland morphogenesis / mesenchymal cell differentiation involved in lung development / lacrimal gland development / otic vesicle formation / prostate gland morphogenesis / regulation of smooth muscle cell differentiation / regulation of morphogenesis of a branching structure / orbitofrontal cortex development / squamous basal epithelial stem cell differentiation involved in prostate gland acinus development / embryonic organ morphogenesis / branching morphogenesis of a nerve / endochondral bone growth / morphogenesis of embryonic epithelium / epidermis morphogenesis / bud elongation involved in lung branching / mesonephric epithelium development / branch elongation involved in ureteric bud branching / positive regulation of epithelial cell proliferation involved in lung morphogenesis / pyramidal neuron development / regulation of endothelial tube morphogenesis / membranous septum morphogenesis / reproductive structure development / limb bud formation / FGFR3b ligand binding and activation / lung lobe morphogenesis / gland morphogenesis / regulation of endothelial cell chemotaxis to fibroblast growth factor / fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development / ventricular zone neuroblast division / embryonic digestive tract morphogenesis / epithelial cell proliferation involved in salivary gland morphogenesis / mesenchymal cell differentiation / branching involved in prostate gland morphogenesis / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / mesenchymal cell proliferation involved in lung development / branching involved in labyrinthine layer morphogenesis / 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 / regulation of osteoblast proliferation / Phospholipase C-mediated cascade; FGFR2 / FGFR4 ligand binding and activation / FGFR1b ligand binding and activation / fibroblast growth factor receptor activity / embryonic pattern specification / Phospholipase C-mediated cascade; FGFR4 / branching involved in salivary gland morphogenesis / outflow tract septum 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 / mesodermal cell differentiation / regulation of smoothened signaling pathway / embryonic cranial skeleton morphogenesis / digestive tract development / positive regulation of hepatocyte proliferation / bone morphogenesis / S100 protein binding / skeletal system morphogenesis / odontogenesis / positive regulation of intracellular signal transduction / positive regulation of mesenchymal cell proliferation / ventricular cardiac muscle tissue morphogenesis / ureteric bud development / regulation of osteoblast differentiation / Signaling by FGFR2 IIIa TM / inner ear morphogenesis / midbrain development / organ growth / hair follicle morphogenesis / cell fate commitment / PI-3K cascade:FGFR3 / lung alveolus development / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / PI-3K cascade:FGFR2 / bone mineralization / fibroblast growth factor binding / prostate epithelial cord elongation / PI-3K cascade:FGFR4 / positive regulation of sprouting angiogenesis / PI-3K cascade:FGFR1 / positive regulation of cell division / excitatory synapse / positive regulation of Wnt signaling pathway Similarity search - Function | |||||||||
Biological species | HOMO SAPIENS (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å | |||||||||
Authors | Pellegrini, L. / Burke, D.F. / von Delft, F. / Mulloy, B. / Blundell, T.L. | |||||||||
Citation | Journal: Nature / Year: 2000 Title: Crystal Structure of Fibroblast Growth Factor Receptor Ectodomain Bound to Ligand and Heparin Authors: Pellegrini, L. / Burke, D.F. / von Delft, F. / Mulloy, B. / Blundell, T.L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1e0o.cif.gz | 143.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1e0o.ent.gz | 115.1 KB | Display | PDB format |
PDBx/mmJSON format | 1e0o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1e0o_validation.pdf.gz | 505.6 KB | Display | wwPDB validaton report |
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Full document | 1e0o_full_validation.pdf.gz | 542 KB | Display | |
Data in XML | 1e0o_validation.xml.gz | 20 KB | Display | |
Data in CIF | 1e0o_validation.cif.gz | 29.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e0/1e0o ftp://data.pdbj.org/pub/pdb/validation_reports/e0/1e0o | 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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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
-FIBROBLAST GROWTH FACTOR ... , 2 types, 4 molecules ACBD
#1: Protein | Mass: 15857.864 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Description: RECOMBINANT / Plasmid: PET14A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P05230 #2: Protein | Mass: 24526.830 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Description: RECOMBINANT / Plasmid: PET3A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P21802 |
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-Sugars , 1 types, 1 molecules
#3: Polysaccharide | 2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose- ...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-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-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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-Non-polymers , 3 types, 51 molecules
#4: Chemical | ChemComp-NI / #5: Chemical | ChemComp-SO4 / #6: 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: 4.5 Å3/Da / Density % sol: 72 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.5 Details: CRYSTALS WERE GROWN FROM: 1.0M LI2SO4, 0.1M TRISCL PH=8.5, 10MM NISO4, pH 8.50 | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / pH: 7.2 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 15, 1999 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→24.2 Å / Num. obs: 36342 / % possible obs: 98.3 % / Redundancy: 3.5 % / Rsym value: 0.084 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 2.8→2.95 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 1.7 / Rsym value: 0.474 / % possible all: 100 |
Reflection | *PLUS Num. measured all: 127885 / Rmerge(I) obs: 0.084 |
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.474 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.8→24.2 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 69.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→24.2 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.242 / Rfactor Rfree: 0.28 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |