+Open data
-Basic information
Entry | Database: PDB / ID: 4dke | |||||||||
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Title | Crystal Structure of Human Interleukin-34 Bound to FAb1.1 | |||||||||
Components |
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Keywords | CYTOKINE/IMMUNE SYSTEM / dimeric four-helix bundle cytokine / IgG / glycosylation / CYTOKINE-IMMUNE SYSTEM complex | |||||||||
Function / homology | Function and homology information interleukin-34-mediated signaling pathway / macrophage colony-stimulating factor receptor binding / microglial cell proliferation / positive regulation of macrophage differentiation / positive regulation of monocyte differentiation / positive regulation of macrophage proliferation / Other interleukin signaling / positive regulation of oligodendrocyte differentiation / positive regulation of macrophage chemotaxis / positive regulation of protein tyrosine kinase activity ...interleukin-34-mediated signaling pathway / macrophage colony-stimulating factor receptor binding / microglial cell proliferation / positive regulation of macrophage differentiation / positive regulation of monocyte differentiation / positive regulation of macrophage proliferation / Other interleukin signaling / positive regulation of oligodendrocyte differentiation / positive regulation of macrophage chemotaxis / positive regulation of protein tyrosine kinase activity / cytokine activity / positive regulation of MAP kinase activity / growth factor activity / Signaling by CSF1 (M-CSF) in myeloid cells / inflammatory response / positive regulation of protein phosphorylation / innate immune response / positive regulation of cell population proliferation / positive regulation of gene expression / extracellular space / extracellular region / identical protein binding Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | |||||||||
Authors | Ma, X. / Chen, Y. / Stawicki, S. / Wu, Y. / Bazan, J.F. / Starovasnik, M.A. | |||||||||
Citation | Journal: Structure / Year: 2012 Title: Structural Basis for the Dual Recognition of Helical Cytokines IL-34 and CSF-1 by CSF-1R. Authors: Ma, X. / Lin, W.Y. / Chen, Y. / Stawicki, S. / Mukhyala, K. / Wu, Y. / Martin, F. / Bazan, J.F. / Starovasnik, M.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4dke.cif.gz | 229.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4dke.ent.gz | 187 KB | Display | PDB format |
PDBx/mmJSON format | 4dke.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4dke_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 4dke_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 4dke_validation.xml.gz | 43.4 KB | Display | |
Data in CIF | 4dke_validation.cif.gz | 59.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dk/4dke ftp://data.pdbj.org/pub/pdb/validation_reports/dk/4dke | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Antibody , 2 types, 4 molecules HILM
#2: Antibody | Mass: 24433.375 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: PROTEIN SELECTED BY PHAGE DISPLAY / Production host: Cricetulus griseus (Chinese hamster) #3: Antibody | Mass: 23396.924 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: PROTEIN SELECTED BY PHAGE DISPLAY / Production host: Cricetulus griseus (Chinese hamster) |
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-Protein / Non-polymers , 2 types, 52 molecules AB
#1: Protein | Mass: 21860.846 Da / Num. of mol.: 2 / Fragment: active core Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IL34, C16orf77 / Cell line (production host): Tni PRO / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q6ZMJ4 #6: Water | ChemComp-HOH / | |
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-Sugars , 2 types, 2 molecules
#4: Polysaccharide | alpha-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]alpha-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 |
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#5: Polysaccharide | beta-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...beta-D-mannopyranose-(1-6)-alpha-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 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.46 Å3/Da / Density % sol: 64.43 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2 M Ammonium phosphate monobasic, 0.1 M Tris pH 8.5, 50% v/v (+/-)-2-Methyl-2,4-pentanediol, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 18, 2011 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.99→50 Å / Num. obs: 38972 / % possible obs: 99.6 % / Redundancy: 5.4 % / Rsym value: 0.086 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 2.99→3.11 Å / Redundancy: 5 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.623 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→50 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.906 / Cross valid method: THROUGHOUT / ESU R: 4.29 / ESU R Free: 0.405 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 67.841 Å2
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Refinement step | Cycle: LAST / Resolution: 3→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.078 Å / Total num. of bins used: 20
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