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Yorodumi- PDB-1djs: LIGAND-BINDING PORTION OF FIBROBLAST GROWTH FACTOR RECEPTOR 2 IN ... -
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-Basic information
Entry | Database: PDB / ID: 1djs | ||||||
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Title | LIGAND-BINDING PORTION OF FIBROBLAST GROWTH FACTOR RECEPTOR 2 IN COMPLEX WITH FGF1 | ||||||
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Keywords | HORMONE/GROWTH FACTOR/RECEPTOR / FGFR / FGF / IMMUNOGLOBULIN / IMMUNE SYSTEM / HORMONE-GROWTH FACTOR-RECEPTOR COMPLEX | ||||||
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 / orbitofrontal cortex development / regulation of morphogenesis of a branching structure / squamous basal epithelial stem cell differentiation involved in prostate gland acinus development / branching morphogenesis of a nerve / embryonic organ morphogenesis / 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 / membranous septum morphogenesis / regulation of endothelial tube morphogenesis / FGFR3b ligand binding and activation / reproductive structure development / limb bud formation / lung lobe morphogenesis / gland morphogenesis / fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development / ventricular zone neuroblast division / regulation of endothelial cell chemotaxis to fibroblast growth factor / embryonic digestive tract morphogenesis / epithelial cell proliferation involved in salivary gland morphogenesis / mesenchymal cell differentiation / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / branching involved in prostate gland morphogenesis / mesenchymal cell proliferation involved in lung development / Phospholipase C-mediated cascade; FGFR3 / branching involved in labyrinthine layer morphogenesis / 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 / fibroblast growth factor receptor activity / FGFR1b ligand binding and activation / branching involved in salivary gland morphogenesis / Phospholipase C-mediated cascade; FGFR4 / embryonic pattern specification / Signaling by activated point mutants of FGFR1 / outflow tract septum morphogenesis / 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 / digestive tract development / regulation of smoothened signaling pathway / embryonic cranial skeleton morphogenesis / positive regulation of hepatocyte proliferation / bone morphogenesis / S100 protein binding / skeletal system morphogenesis / odontogenesis / ureteric bud development / positive regulation of intracellular signal transduction / positive regulation of mesenchymal cell proliferation / regulation of osteoblast differentiation / ventricular cardiac muscle tissue morphogenesis / inner ear morphogenesis / Signaling by FGFR2 IIIa TM / organ growth / midbrain development / hair follicle morphogenesis / lung alveolus development / PI-3K cascade:FGFR3 / fibroblast growth factor binding / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / positive regulation of sprouting angiogenesis / PI-3K cascade:FGFR2 / bone mineralization / prostate epithelial cord elongation / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / positive regulation of cell division / excitatory synapse / positive regulation of Wnt signaling pathway / PI3K Cascade Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å | ||||||
Authors | Stauber, D.J. / Digabriele, A.D. / Hendrickson, W.A. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2000 Title: Structural interactions of fibroblast growth factor receptor with its ligands. Authors: Stauber, D.J. / DiGabriele, A.D. / Hendrickson, W.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1djs.cif.gz | 86.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1djs.ent.gz | 67.4 KB | Display | PDB format |
PDBx/mmJSON format | 1djs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dj/1djs ftp://data.pdbj.org/pub/pdb/validation_reports/dj/1djs | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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: 24298.936 Da / Num. of mol.: 1 / Fragment: IG-LIKE DOMAINS 2 AND 3 / Mutation: N147T,S148L,N149E,N150P,K151E,R152G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P21802, EC: 2.7.1.112 | ||
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#2: Protein | Mass: 15336.096 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P05230 | ||
#3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
-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: 64.2 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: 1.6M AMMONIUM SULFATE, 10MM TRIS (PH7.5), pH 7.50 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / Details: seeding | ||||||||||||||||||||||||||||||
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: 0.9919, 0.9793, 0.9791, 0.9641 | |||||||||||||||
Detector | Type: ADSC QUANTUM 4r / Detector: CCD / Date: Jun 17, 1999 | |||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.4→20 Å / Num. obs: 41549 / % possible obs: 99.8 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 11.8 | |||||||||||||||
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 4 % / Rmerge(I) obs: 0.402 / % possible all: 99.9 | |||||||||||||||
Reflection | *PLUS Num. measured all: 180297 | |||||||||||||||
Reflection shell | *PLUS % possible obs: 99.9 % |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.4→6 Å / SU B: 5.181 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.449 / ESU R Free: 0.298
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Displacement parameters | Biso mean: 29.47 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→6 Å
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Refine LS restraints |
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