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Open data
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Basic information
Entry | Database: PDB / ID: 4exp | ||||||
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Title | Structure of mouse Interleukin-34 in complex with mouse FMS | ||||||
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![]() | CYTOKINE/TRANSFERASE / extended 4-helix bundle / immunoglobunin / beta-sandwich / CYTOKINE-TRANSFERASE complex | ||||||
Function / homology | ![]() regulation of mononuclear cell proliferation / negative regulation of platelet formation / interleukin-34-mediated signaling pathway / Other interleukin signaling / positive regulation of astrocyte activation / macrophage colony-stimulating factor receptor binding / monocyte homeostasis / positive regulation of macrophage migration / macrophage colony-stimulating factor receptor activity / forebrain neuron differentiation ...regulation of mononuclear cell proliferation / negative regulation of platelet formation / interleukin-34-mediated signaling pathway / Other interleukin signaling / positive regulation of astrocyte activation / macrophage colony-stimulating factor receptor binding / monocyte homeostasis / positive regulation of macrophage migration / macrophage colony-stimulating factor receptor activity / forebrain neuron differentiation / CSF1-CSF1R complex / macrophage colony-stimulating factor signaling pathway / cell-cell junction maintenance / positive regulation of lymphocyte proliferation / regulation of macrophage migration / cellular response to macrophage colony-stimulating factor stimulus / negative regulation of myotube differentiation / organic cyclic compound binding / positive regulation of myoblast proliferation / positive regulation of cell cycle G1/S phase transition / microglial cell proliferation / positive regulation of macrophage differentiation / olfactory bulb development / dentate gyrus development / positive regulation of leukocyte proliferation / positive regulation by host of viral process / neutrophil homeostasis / ruffle organization / positive regulation of monocyte differentiation / positive regulation of osteoclast differentiation / microglia development / positive regulation of macrophage proliferation / regulation of bone resorption / positive regulation of cell motility / neuron projection extension / negative regulation of epithelial cell differentiation / positive regulation of oligodendrocyte differentiation / positive regulation of macrophage chemotaxis / cytokine binding / growth factor binding / cellular response to cytokine stimulus / regulation of MAPK cascade / hemopoiesis / positive regulation of bone mineralization / positive regulation of chemokine production / positive regulation of tyrosine phosphorylation of STAT protein / cell surface receptor protein tyrosine kinase signaling pathway / transmembrane receptor protein tyrosine kinase activity / osteoclast differentiation / cytokine activity / response to ischemia / regulation of actin cytoskeleton organization / axon guidance / microglial cell activation / growth factor activity / receptor protein-tyrosine kinase / cytokine-mediated signaling pathway / peptidyl-tyrosine phosphorylation / positive regulation of tumor necrosis factor production / regulation of cell shape / cell body / perikaryon / protein phosphatase binding / protein tyrosine kinase activity / cell population proliferation / protein autophosphorylation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / receptor complex / positive regulation of cell migration / inflammatory response / positive regulation of protein phosphorylation / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / innate immune response / positive regulation of cell population proliferation / positive regulation of gene expression / negative regulation of apoptotic process / cell surface / protein homodimerization activity / extracellular space / nucleoplasm / ATP binding / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Liu, H. / Leo, C. / Chen, X. / Wong, B.R. / Williams, L.T. / Lin, H. / He, X. | ||||||
![]() | ![]() Title: The mechanism of shared but distinct CSF-1R signaling by the non-homologous cytokines IL-34 and CSF-1. Authors: Liu, H. / Leo, C. / Chen, X. / Wong, B.R. / Williams, L.T. / Lin, H. / He, X. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 110 KB | Display | ![]() |
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PDB format | ![]() | 83.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 459.4 KB | Display | ![]() |
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Full document | ![]() | 474.8 KB | Display | |
Data in XML | ![]() | 22.6 KB | Display | |
Data in CIF | ![]() | 31.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4exnSC ![]() 3ejjS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 20547.934 Da / Num. of mol.: 1 / Fragment: UNP residues 21-194 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Protein | Mass: 31223.330 Da / Num. of mol.: 1 / Fragment: UNP residues 20-298 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P09581, receptor protein-tyrosine kinase | ||
#3: Sugar | ChemComp-NAG / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 58.63 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 20% PEG3000, 0.1 M sodium acetate, 0.2 M lithium sulfate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 15, 2009 |
Radiation | Monochromator: Kohzu Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. all: 15606 / Num. obs: 15606 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.466 / Mean I/σ(I) obs: 2.6 / Num. unique all: 1503 / % possible all: 96.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRIES 4EXN AND 3EJJ Resolution: 2.8→50 Å / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 55.4216 Å2 | ||||||||||||||||||||
Displacement parameters | Biso max: 150.62 Å2 / Biso mean: 85.7185 Å2 / Biso min: 6.04 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.91 Å /
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Xplor file |
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