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Open data
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Basic information
Entry | Database: PDB / ID: 6aez | |||||||||
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Title | Crystal structure of human CCL5 trimer | |||||||||
![]() | (C-C motif chemokine 5) x 2 | |||||||||
![]() | CYTOKINE / CCL5 / RANTES / Chemokine / Oligomer / dimer / CC-type | |||||||||
Function / homology | ![]() regulation of chronic inflammatory response / CCR4 chemokine receptor binding / chemokine receptor antagonist activity / activation of phospholipase D activity / positive regulation of cellular biosynthetic process / CCR1 chemokine receptor binding / positive regulation of natural killer cell chemotaxis / negative regulation of macrophage apoptotic process / chemokine receptor binding / positive regulation of cell-cell adhesion mediated by integrin ...regulation of chronic inflammatory response / CCR4 chemokine receptor binding / chemokine receptor antagonist activity / activation of phospholipase D activity / positive regulation of cellular biosynthetic process / CCR1 chemokine receptor binding / positive regulation of natural killer cell chemotaxis / negative regulation of macrophage apoptotic process / chemokine receptor binding / positive regulation of cell-cell adhesion mediated by integrin / positive regulation of activation of Janus kinase activity / receptor signaling protein tyrosine kinase activator activity / CCR5 chemokine receptor binding / positive regulation of T cell chemotaxis / positive regulation of homotypic cell-cell adhesion / negative regulation of G protein-coupled receptor signaling pathway / CCR chemokine receptor binding / lymphocyte chemotaxis / phosphatidylinositol phospholipase C activity / negative regulation of T cell apoptotic process / positive regulation of T cell apoptotic process / neutrophil activation / positive regulation of calcium ion transport / eosinophil chemotaxis / positive regulation of innate immune response / cellular response to fibroblast growth factor stimulus / chemokine-mediated signaling pathway / positive regulation of monocyte chemotaxis / Chemokine receptors bind chemokines / chemokine activity / dendritic cell chemotaxis / regulation of T cell activation / leukocyte cell-cell adhesion / negative regulation of viral genome replication / phospholipase activator activity / positive regulation of macrophage chemotaxis / positive regulation of smooth muscle cell migration / exocytosis / chemoattractant activity / macrophage chemotaxis / Interleukin-10 signaling / monocyte chemotaxis / regulation of insulin secretion / positive regulation of cell adhesion / negative regulation by host of viral transcription / positive regulation of T cell migration / positive regulation of translational initiation / positive regulation of viral genome replication / cellular response to interleukin-1 / positive regulation of T cell proliferation / positive regulation of phosphorylation / positive regulation of tyrosine phosphorylation of STAT protein / neutrophil chemotaxis / epithelial cell proliferation / positive regulation of epithelial cell proliferation / positive regulation of smooth muscle cell proliferation / positive regulation of receptor signaling pathway via JAK-STAT / response to virus / response to toxic substance / cellular response to virus / cellular response to type II interferon / intracellular calcium ion homeostasis / calcium ion transport / chemotaxis / : / cell-cell signaling / cellular response to tumor necrosis factor / G alpha (i) signalling events / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / protein kinase activity / positive regulation of cell migration / inflammatory response / G protein-coupled receptor signaling pathway / protein homodimerization activity / extracellular space / extracellular region / identical protein binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Chen, Y.C. / Li, K.M. / Chen, P.J. / Zarivach, R. / Sun, Y.J. / Sue, S.C. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Integrative Model to Coordinate the Oligomerization and Aggregation Mechanisms of CCL5. Authors: Chen, Y.C. / Chen, S.P. / Li, J.Y. / Chen, P.C. / Lee, Y.Z. / Li, K.M. / Zarivach, R. / Sun, Y.J. / Sue, S.C. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2018 Title: Human CCL5 trimer: expression, purification and initial crystallographic studies. Authors: Chen, Y.C. / Li, K.M. / Zarivach, R. / Sun, Y.J. / Sue, S.C. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 100.3 KB | Display | ![]() |
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PDB format | ![]() | 76.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 460.6 KB | Display | ![]() |
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Full document | ![]() | 463.8 KB | Display | |
Data in XML | ![]() | 12.8 KB | Display | |
Data in CIF | ![]() | 17.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5yamC ![]() 1eqtS S: Starting model for refinement C: citing same article ( |
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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 on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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Details | AUTHOR DETERMINED BIOLOGICAL ASSEMBLY: UNKNOWN. |
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Components
#1: Protein | Mass: 7951.170 Da / Num. of mol.: 2 / Mutation: E67S Source method: isolated from a genetically manipulated source Details: The CCL5 trimer was prepared by mixing native protein (E67) and mutant (S67) with molar ratio of 1:2. Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | | Mass: 7993.207 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.3 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 0.2M ammonium sulfate, 0.1M BIS-TRIS pH 5, 16% (w/v) polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 19, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.63→53.09 Å / Num. obs: 30546 / % possible obs: 94.9 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 48.73 |
Reflection shell | Resolution: 1.63→1.66 Å / Rmerge(I) obs: 0.889 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1EQT monomer Resolution: 1.63→53.09 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.952 / SU B: 5.531 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.096 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.535 Å2
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Refinement step | Cycle: 1 / Resolution: 1.63→53.09 Å
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Refine LS restraints |
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