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Yorodumi- PDB-2fdb: Crystal Structure of Fibroblast growth factor (FGF)8b in complex ... -
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-Basic information
Entry | Database: PDB / ID: 2fdb | ||||||
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Title | Crystal Structure of Fibroblast growth factor (FGF)8b in complex with FGF Receptor (FGFR) 2c | ||||||
Components |
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Keywords | HORMONE/GROWTH FACTOR/TRANSFERASE / beta-trefoil fold / immunoglobulin fold / HORMONE-GROWTH FACTOR-TRANSFERASE COMPLEX | ||||||
Function / homology | Function and homology information pallium development / midbrain-hindbrain boundary development / negative regulation of cardiac muscle tissue development / subpallium development / larynx morphogenesis / FGFR3 mutant receptor activation / neural plate morphogenesis / type 2 fibroblast growth factor receptor binding / mesodermal cell migration / cell migration involved in mesendoderm migration ...pallium development / midbrain-hindbrain boundary development / negative regulation of cardiac muscle tissue development / subpallium development / larynx morphogenesis / FGFR3 mutant receptor activation / neural plate morphogenesis / type 2 fibroblast growth factor receptor binding / mesodermal cell migration / cell migration involved in mesendoderm migration / : / forebrain dorsal/ventral pattern formation / forebrain neuron development / dorsal/ventral axon guidance / type 1 fibroblast growth factor receptor binding / embryonic neurocranium morphogenesis / regulation of odontogenesis of dentin-containing tooth / FGFRL1 modulation of FGFR1 signaling / corticotropin hormone secreting cell differentiation / thyroid-stimulating hormone-secreting cell differentiation / 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 / aorta morphogenesis / orbitofrontal cortex development / regulation of morphogenesis of a branching structure / gonad development / epithelial to mesenchymal transition involved in endocardial cushion formation / cell proliferation in forebrain / 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 / response to xenobiotic stimulus => GO:0009410 / positive regulation of epithelial cell proliferation involved in lung morphogenesis / pyramidal neuron development / mesonephros development / membranous septum morphogenesis / reproductive structure development / limb bud formation / lung lobe morphogenesis / FGFR3b ligand binding and activation / limb morphogenesis / gland morphogenesis / fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development / ventricular zone neuroblast division / embryonic digestive tract morphogenesis / neuroepithelial cell differentiation / epithelial cell proliferation involved in salivary gland morphogenesis / mesenchymal cell differentiation / forebrain morphogenesis / branching involved in prostate gland morphogenesis / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / positive regulation of organ growth / mesenchymal cell proliferation involved in lung development / branching involved in labyrinthine layer morphogenesis / Phospholipase C-mediated cascade; FGFR3 / positive regulation of G protein-coupled receptor signaling pathway / FGFR2b ligand binding and activation / fibroblast growth factor receptor binding / male genitalia development / FGFR2c ligand binding and activation / Activated point mutants of FGFR2 / pharyngeal system development / regulation of osteoblast proliferation / Phospholipase C-mediated cascade; FGFR2 / FGFR4 ligand binding and activation / fibroblast growth factor receptor activity / branching involved in salivary gland morphogenesis / Phospholipase C-mediated cascade; FGFR4 / embryonic pattern specification / outflow tract septum morphogenesis / signal transduction involved in regulation of gene expression / 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 / dopaminergic neuron differentiation / metanephros development / mesodermal cell differentiation / regulation of smoothened signaling pathway / embryonic heart tube development Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å | ||||||
Authors | Mohammadi, M. / Olsen, S.K. | ||||||
Citation | Journal: Genes Dev. / Year: 2006 Title: Structural basis by which alternative splicing modulates the organizer activity of FGF8 in the brain Authors: Olsen, S.K. / Li, J.Y.H. / Bromleigh, C. / Eliseenkova, A.V. / Ibrahimi, O.A. / Lao, Z. / Zhang, F. / Linhardt, R.J. / Joyner, A.L. / Mohammadi, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fdb.cif.gz | 147.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fdb.ent.gz | 111.5 KB | Display | PDB format |
PDBx/mmJSON format | 2fdb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2fdb_validation.pdf.gz | 457.9 KB | Display | wwPDB validaton report |
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Full document | 2fdb_full_validation.pdf.gz | 467.1 KB | Display | |
Data in XML | 2fdb_validation.xml.gz | 27.1 KB | Display | |
Data in CIF | 2fdb_validation.cif.gz | 37.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fd/2fdb ftp://data.pdbj.org/pub/pdb/validation_reports/fd/2fdb | HTTPS FTP |
-Related structure data
Related structure data | 1evtS S: Starting model for refinement |
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Similar 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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Details | There are two biological units. 1) chain A and chain B, and 2) chain C and chain D (i.e. two complexes of FGF8b with FGFR2c |
-Components
#1: Protein | Mass: 18906.648 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P55075 #2: Protein | Mass: 24758.127 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FGFR2, BEK, KSAM / Production host: Escherichia coli (E. coli) References: UniProt: Q9UQH9, UniProt: P21802*PLUS, EC: 2.7.1.112 #3: 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: 2.51 Å3/Da / Density % sol: 51.05 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 18.5% mPEG 5000, 0.15M magnesium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 173 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97925 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 1, 2004 |
Radiation | Monochromator: Kohzu Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97925 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. all: 44825 / Num. obs: 44825 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rsym value: 0.084 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 5.8 % / Num. unique all: 4429 / Rsym value: 0.306 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1EVT Resolution: 2.28→25 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.28→25 Å
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Refine LS restraints |
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