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Yorodumi- PDB-4adq: CRYSTAL STRUCTURE OF THE MOUSE COLONY-STIMULATING FACTOR 1 (MCSF-... -
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-Basic information
Entry | Database: PDB / ID: 4adq | |||||||||
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Title | CRYSTAL STRUCTURE OF THE MOUSE COLONY-STIMULATING FACTOR 1 (MCSF-1) CYTOKINE IN COMPLEX WITH THE VIRAL RECEPTOR BARF1 | |||||||||
Components |
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Keywords | IMMUNE SYSTEM/RECEPTOR / IMMUNE SYSTEM-RECEPTOR COMPLEX / RTKIII / EXTRACELLULAR / CYTOKINE RECEPTOR-CYTOKINE COMPLEX / FOUR-HELIX BUNDLE / GLYCOPROTEIN / IMMUNOGLOBULIN DOMAIN / ONCOGENE / CYTOKINE/SIGNALING | |||||||||
Function / homology | Function and homology information Other interleukin signaling / mammary gland fat development / positive regulation of macrophage colony-stimulating factor signaling pathway / macrophage homeostasis / macrophage colony-stimulating factor receptor binding / monocyte homeostasis / osteoclast proliferation / positive regulation of macrophage migration / positive regulation of odontogenesis of dentin-containing tooth / developmental process involved in reproduction ...Other interleukin signaling / mammary gland fat development / positive regulation of macrophage colony-stimulating factor signaling pathway / macrophage homeostasis / macrophage colony-stimulating factor receptor binding / monocyte homeostasis / osteoclast proliferation / positive regulation of macrophage migration / positive regulation of odontogenesis of dentin-containing tooth / developmental process involved in reproduction / CSF1-CSF1R complex / macrophage colony-stimulating factor signaling pathway / positive regulation of microglial cell migration / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / 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 / positive regulation of mononuclear cell 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 / positive regulation of macrophage proliferation / branching involved in mammary gland duct morphogenesis / positive regulation of leukocyte migration / positive regulation of cell-matrix adhesion / positive regulation of macrophage chemotaxis / monocyte differentiation / macrophage differentiation / regulation of ossification / homeostasis of number of cells within a tissue / positive regulation of protein metabolic process / ossification / osteoclast differentiation / cytokine activity / response to ischemia / growth factor activity / cell surface receptor protein tyrosine kinase signaling pathway / Ras protein signal transduction / nuclear body / positive regulation of cell migration / inflammatory response / 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 / plasma membrane Similarity search - Function | |||||||||
Biological species | Human gammaherpesvirus 4 (Epstein-Barr virus) Mus musculus (house mouse) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.5 Å | |||||||||
Authors | Elegheert, J. / Bracke, N. / Savvides, S.N. | |||||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2012 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4adq.cif.gz | 277.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4adq.ent.gz | 224.3 KB | Display | PDB format |
PDBx/mmJSON format | 4adq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ad/4adq ftp://data.pdbj.org/pub/pdb/validation_reports/ad/4adq | HTTPS FTP |
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-Related structure data
Related structure data | 3uezC 3uf2C 3uf5SC 4adfC 2ch8S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 23412.654 Da / Num. of mol.: 4 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human gammaherpesvirus 4 (Epstein-Barr virus) Strain: B95-8 / Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: P0CW72, UniProt: P03228*PLUS #2: Protein | Mass: 17872.107 Da / Num. of mol.: 4 / Fragment: RESIDUES 21-221 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus / Plasmid: PET15B / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): CODONPLUS RIL / References: UniProt: P07141 #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source Compound details | ENGINEERED RESIDUE IN CHAIN A, THR 169 TO SER ENGINEERED RESIDUE IN CHAIN B, THR 169 TO SER ...ENGINEERED | |
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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: 3.38 Å3/Da / Density % sol: 61.4 % / Description: NONE |
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Crystal grow | pH: 8 / Details: pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97887 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 8, 2011 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97887 Å / Relative weight: 1 |
Reflection | Resolution: 4.5→40 Å / Num. obs: 11082 / % possible obs: 94.5 % / Observed criterion σ(I): 2 / Redundancy: 1.7 % / Biso Wilson estimate: 138.7 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 5.7 |
Reflection shell | Resolution: 4.5→4.62 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 1.6 / % possible all: 93.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 2CH8 AND 3UF5 Resolution: 4.5→117.375 Å / SU ML: 0.58 / σ(F): 1.96 / Phase error: 27.2 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 164.595 Å2 / ksol: 0.346 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 187.44 Å2
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Refinement step | Cycle: LAST / Resolution: 4.5→117.375 Å
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Refine LS restraints |
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LS refinement shell |
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