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- PDB-4liq: Structure of the extracellular domain of human CSF-1 receptor in ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4liq | |||||||||
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Title | Structure of the extracellular domain of human CSF-1 receptor in complex with the Fab fragment of RG7155 | |||||||||
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![]() | IMMUNE SYSTEM / CSF-1 receptor / receptor tyrosine kinase / antibody / fab fragment / IgG like domain | |||||||||
Function / homology | ![]() macrophage colony-stimulating factor receptor activity / forebrain neuron differentiation / CSF1-CSF1R complex / macrophage colony-stimulating factor signaling pathway / cell-cell junction maintenance / regulation of macrophage migration / cellular response to macrophage colony-stimulating factor stimulus / microglial cell proliferation / olfactory bulb development / mammary gland duct morphogenesis ...macrophage colony-stimulating factor receptor activity / forebrain neuron differentiation / CSF1-CSF1R complex / macrophage colony-stimulating factor signaling pathway / cell-cell junction maintenance / regulation of macrophage migration / cellular response to macrophage colony-stimulating factor stimulus / microglial cell proliferation / olfactory bulb development / mammary gland duct morphogenesis / positive regulation by host of viral process / ruffle organization / positive regulation of macrophage proliferation / regulation of bone resorption / positive regulation of cell motility / Other interleukin signaling / positive regulation of macrophage chemotaxis / cytokine binding / growth factor binding / cellular response to cytokine stimulus / monocyte differentiation / regulation of MAPK cascade / macrophage differentiation / hemopoiesis / positive regulation of protein tyrosine kinase activity / Transcriptional Regulation by VENTX / positive regulation of chemokine production / positive regulation of tyrosine phosphorylation of STAT protein / cell surface receptor protein tyrosine kinase signaling pathway / osteoclast differentiation / response to ischemia / regulation of actin cytoskeleton organization / axon guidance / receptor protein-tyrosine kinase / cytokine-mediated signaling pathway / peptidyl-tyrosine phosphorylation / Signaling by CSF1 (M-CSF) in myeloid cells / regulation of cell shape / 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 / negative regulation of apoptotic process / cell surface / signal transduction / protein homodimerization activity / nucleoplasm / ATP binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Benz, J. / Gorr, I.H. / Hertenberger, H. / Ries, C.H. | |||||||||
![]() | ![]() Title: Targeting tumor-associated macrophages with anti-CSF-1R antibody reveals a strategy for cancer therapy Authors: Ries, C.H. / Cannarile, M.A. / Hoves, S. / Benz, J. / Wartha, K. / Runza, V. / Rey-Giraud, F. / Pradel, L.P. / Feuerhake, F. / Klaman, I. / Jones, T. / Jucknischke, U. / Scheiblich, S. / ...Authors: Ries, C.H. / Cannarile, M.A. / Hoves, S. / Benz, J. / Wartha, K. / Runza, V. / Rey-Giraud, F. / Pradel, L.P. / Feuerhake, F. / Klaman, I. / Jones, T. / Jucknischke, U. / Scheiblich, S. / Kaluza, K. / Gorr, I.H. / Walz, A. / Abiraj, K. / Cassier, P.A. / Sica, A. / Gomez-Roca, C. / de Visser, K.E. / Italiano, A. / Le Tourneau, C. / Delord, J.P. / Levitsky, H. / Blay, J.Y. / Ruttinger, D. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 367.6 KB | Display | ![]() |
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PDB format | ![]() | 295.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 34.5 KB | Display | |
Data in CIF | ![]() | 49.2 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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Unit cell |
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Components
-Protein , 1 types, 1 molecules E
#1: Protein | Mass: 61172.742 Da / Num. of mol.: 1 / Fragment: ectodomain, UNP residues 2-512 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: P07333, receptor protein-tyrosine kinase |
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-Antibody , 2 types, 2 molecules HL
#2: Antibody | Mass: 23845.668 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Humanized Version of a monoclonal murine. / Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#3: Antibody | Mass: 23381.848 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Humanized Version of a monoclonal murine. / Source: (gene. exp.) ![]() ![]() ![]() ![]() |
-Sugars , 3 types, 3 molecules ![](data/chem/img/NAG.gif)
#4: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#5: Polysaccharide | alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#6: Sugar | ChemComp-NAG / |
-Non-polymers , 2 types, 269 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#7: Chemical | ChemComp-SO4 / |
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#8: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.16 Å3/Da / Density % sol: 61.03 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 25% PEG 3350, 0.2M lithium sulfate, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 20, 2010 |
Radiation | Monochromator: Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.55→145 Å / Num. all: 45538 / Num. obs: 45526 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1.4 / Redundancy: 6.7 % / Biso Wilson estimate: 73.39 Å2 / Rmerge(I) obs: 0.119 |
Reflection shell | Resolution: 2.55→2.65 Å / Redundancy: 6.93 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 1.4 / Num. unique all: 4883 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3EJJ, 2EC8 Resolution: 2.6→38.07 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.9128 / SU R Cruickshank DPI: 0.351 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 57.82 Å2
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Refine analyze | Luzzati coordinate error obs: 0.323 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→38.07 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.67 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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