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- PDB-3uf2: Crystal structure of the human Colony-Stimulating Factor 1 (hCSF-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3uf2 | ||||||
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Title | Crystal structure of the human Colony-Stimulating Factor 1 (hCSF-1) cytokine | ||||||
![]() | Macrophage colony-stimulating factor 1 | ||||||
![]() | CYTOKINE / hematopoietic cytokine / RTKIII / Four-helix bundle | ||||||
Function / homology | ![]() regulation of macrophage derived foam cell differentiation / mammary gland fat development / positive regulation of macrophage colony-stimulating factor signaling pathway / macrophage homeostasis / monocyte activation / macrophage colony-stimulating factor receptor binding / monocyte homeostasis / osteoclast proliferation / positive regulation of macrophage migration / developmental process involved in reproduction ...regulation of macrophage derived foam cell differentiation / mammary gland fat development / positive regulation of macrophage colony-stimulating factor signaling pathway / macrophage homeostasis / monocyte activation / macrophage colony-stimulating factor receptor binding / monocyte homeostasis / osteoclast proliferation / positive regulation of macrophage migration / developmental process involved in reproduction / positive regulation of odontogenesis of dentin-containing tooth / CSF1-CSF1R complex / macrophage colony-stimulating factor signaling pathway / positive regulation of microglial cell migration / mammary duct terminal end bud growth / microglial cell proliferation / positive regulation of macrophage differentiation / positive regulation of macrophage derived foam cell differentiation / positive regulation of mononuclear cell proliferation / myeloid leukocyte migration / neutrophil homeostasis / positive regulation of multicellular organism growth / positive regulation of monocyte differentiation / positive regulation of osteoclast differentiation / positive regulation of Ras protein signal transduction / branching involved in mammary gland duct morphogenesis / positive regulation of cell-matrix adhesion / Other interleukin signaling / positive regulation of macrophage chemotaxis / Interleukin-10 signaling / monocyte differentiation / macrophage differentiation / regulation of ossification / positive regulation of protein kinase activity / homeostasis of number of cells within a tissue / cell surface receptor protein tyrosine kinase signaling pathway / positive regulation of protein metabolic process / osteoclast differentiation / cytokine activity / response to ischemia / Post-translational protein phosphorylation / growth factor activity / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Signaling by CSF1 (M-CSF) in myeloid cells / Ras protein signal transduction / nuclear body / positive regulation of cell migration / inflammatory response / endoplasmic reticulum lumen / innate immune response / positive regulation of cell population proliferation / positive regulation of gene expression / perinuclear region of cytoplasm / protein homodimerization activity / extracellular space / extracellular region / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Elegheert, J. / Savvides, S.N. | ||||||
![]() | ![]() Title: Allosteric competitive inactivation of hematopoietic CSF-1 signaling by the viral decoy receptor BARF1 Authors: Elegheert, J. / Bracke, N. / Pouliot, P. / Gutsche, I. / Shkumatov, A.V. / Tarbouriech, N. / Verstraete, K. / Bekaert, A. / Burmeister, W.P. / Svergun, D.I. / Lambrecht, B.N. / Vergauwen, B. / Savvides, S.N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 285.8 KB | Display | ![]() |
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PDB format | ![]() | 242.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 479.9 KB | Display | ![]() |
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Full document | ![]() | 485.2 KB | Display | |
Data in XML | ![]() | 47.7 KB | Display | |
Data in CIF | ![]() | 64.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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5 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 17868.219 Da / Num. of mol.: 10 / Fragment: UNP RESIDUES 33-181 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.65 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 0.1M magnesium chloride, 0.1M sodium citrate pH 5.0, 15% w/v PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 18, 2009 |
Radiation | Monochromator: Bartels Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.75→40 Å / Num. all: 36596 / Num. obs: 36596 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 2.75→3 Å / % possible all: 98.9 |
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Processing
Software | Name: PHENIX / Version: (phenix.refine: dev_874) / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.94 Å2 / ksol: 0.325 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.75→24.942 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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