[English] 日本語
Yorodumi- PDB-4adf: CRYSTAL STRUCTURE OF THE HUMAN COLONY-STIMULATING FACTOR 1 (hCSF-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4adf | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF THE HUMAN COLONY-STIMULATING FACTOR 1 (hCSF-1) CYTOKINE IN COMPLEX WITH THE VIRAL RECEPTOR BARF1 | |||||||||
Components |
| |||||||||
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 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 | HUMAN HERPESVIRUS 4 (Epstein-Barr virus) HOMO SAPIENS (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.4 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4adf.cif.gz | 806.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4adf.ent.gz | 672.4 KB | Display | PDB format |
PDBx/mmJSON format | 4adf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4adf_validation.pdf.gz | 3.5 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4adf_full_validation.pdf.gz | 3.5 MB | Display | |
Data in XML | 4adf_validation.xml.gz | 131.2 KB | Display | |
Data in CIF | 4adf_validation.cif.gz | 173.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ad/4adf ftp://data.pdbj.org/pub/pdb/validation_reports/ad/4adf | HTTPS FTP |
-Related structure data
Related structure data | 3uezC 3uf2SC 3uf5C 4adqC 2ch8S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
2 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
|
-Components
#1: Protein | Mass: 23412.654 Da / Num. of mol.: 12 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HUMAN HERPESVIRUS 4 (Epstein-Barr virus) Strain: B95-8 / Cell line (production host): HEK293T / Production host: HOMO SAPIENS (human) / References: UniProt: P0CW72, UniProt: P03228*PLUS #2: Protein | Mass: 17868.219 Da / Num. of mol.: 12 / Fragment: UNP RESIDUES 33-181 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODONPLUS RIL / References: UniProt: P09603 #3: Polysaccharide | alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[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 #4: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[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 #5: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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 | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 4.6 Å3/Da / Density % sol: 74.1 % / Description: NONE |
---|---|
Crystal grow | pH: 8.5 Details: 0.1 M TRIS HCL, PH 8.50, 1.0 M AMMONIUM PHOSPHATE MONOBASIC |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9714 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 11, 2009 |
Radiation | Monochromator: BARTELS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9714 Å / Relative weight: 1 |
Reflection | Resolution: 4.4→75.85 Å / Num. obs: 58151 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Biso Wilson estimate: 165.84 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 4.4→4.51 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 2.8 / % possible all: 98.2 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 2CH8, 3UF2 Resolution: 4.4→75.847 Å / SU ML: 0.45 / σ(F): 1.34 / Phase error: 27.5 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 187.195 Å2 / ksol: 0.317 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 216.8 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 4.4→75.847 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|