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Open data
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Basic information
Entry | Database: PDB / ID: 5eki | |||||||||
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Title | Crystal Structure of Truncated CCL21 | |||||||||
![]() | C-C motif chemokine 21 | |||||||||
![]() | IMMUNE SYSTEM / Cytokine / Chemokine / Chemotaxis / Inflammation | |||||||||
Function / homology | ![]() mesangial cell-matrix adhesion / dendritic cell dendrite assembly / negative regulation of dendritic cell dendrite assembly / CCR7 chemokine receptor binding / positive regulation of myeloid dendritic cell chemotaxis / chemokine (C-C motif) ligand 21 signaling pathway / positive regulation of dendritic cell antigen processing and presentation / response to prostaglandin E / negative regulation of leukocyte tethering or rolling / establishment of T cell polarity ...mesangial cell-matrix adhesion / dendritic cell dendrite assembly / negative regulation of dendritic cell dendrite assembly / CCR7 chemokine receptor binding / positive regulation of myeloid dendritic cell chemotaxis / chemokine (C-C motif) ligand 21 signaling pathway / positive regulation of dendritic cell antigen processing and presentation / response to prostaglandin E / negative regulation of leukocyte tethering or rolling / establishment of T cell polarity / positive regulation of glycoprotein biosynthetic process / chemokine receptor binding / immunological synapse formation / positive regulation of T cell chemotaxis / positive regulation of pseudopodium assembly / CCR chemokine receptor binding / lymphocyte chemotaxis / positive regulation of chemotaxis / negative regulation of dendritic cell apoptotic process / cellular response to chemokine / ruffle organization / chemokine-mediated signaling pathway / positive regulation of neutrophil chemotaxis / Chemokine receptors bind chemokines / positive regulation of cell motility / chemokine activity / positive regulation of cell adhesion mediated by integrin / dendritic cell chemotaxis / positive regulation of filopodium assembly / positive regulation of cell-matrix adhesion / positive regulation of actin filament polymerization / monocyte chemotaxis / positive regulation of T cell migration / cellular response to interleukin-1 / release of sequestered calcium ion into cytosol / cell maturation / T cell costimulation / neutrophil chemotaxis / cell chemotaxis / positive regulation of JNK cascade / cellular response to type II interferon / positive regulation of receptor-mediated endocytosis / cell-cell signaling / cellular response to tumor necrosis factor / G alpha (i) signalling events / positive regulation of canonical NF-kappaB signal transduction / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / inflammatory response / immune response / G protein-coupled receptor signaling pathway / extracellular space / extracellular region Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Lewandowski, E.M. / Smith, E.W. / Chen, Y. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystallographic Structure of Truncated CCL21 and the Putative Sulfotyrosine-Binding Site. Authors: Smith, E.W. / Lewandowski, E.M. / Moussouras, N.A. / Kroeck, K.G. / Volkman, B.F. / Veldkamp, C.T. / Chen, Y. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 96.5 KB | Display | ![]() |
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PDB format | ![]() | 78.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 477.3 KB | Display | ![]() |
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Full document | ![]() | 477.9 KB | Display | |
Data in XML | ![]() | 18.3 KB | Display | |
Data in CIF | ![]() | 26.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar 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
#1: Protein | Mass: 8864.284 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.06 Å3/Da / Density % sol: 40.31 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: Ammonium sulfate, MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 10, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.903→57.24 Å / Num. obs: 34110 / % possible obs: 99.9 % / Redundancy: 7 % / Net I/σ(I): 16.54 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 2.2 / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 23.489 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→57.24 Å
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