+Open data
-Basic information
Entry | Database: PDB / ID: 6aez | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of human CCL5 trimer | |||||||||
Components | (C-C motif chemokine 5Chemokine) x 2 | |||||||||
Keywords | CYTOKINE / CCL5 / RANTES / Chemokine / Oligomer / dimer / CC-type | |||||||||
Function / homology | Function and homology information 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 / positive regulation of homotypic cell-cell adhesion / CCR5 chemokine receptor binding / positive regulation of T cell chemotaxis / negative regulation of G protein-coupled receptor signaling pathway / CCR chemokine receptor binding / lymphocyte chemotaxis / neutrophil activation / phosphatidylinositol phospholipase C activity / negative regulation of T cell apoptotic process / positive regulation of T cell apoptotic process / 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 / positive regulation of macrophage chemotaxis / negative regulation of viral genome replication / phospholipase activator activity / macrophage chemotaxis / positive regulation of smooth muscle cell migration / exocytosis / chemoattractant activity / Interleukin-10 signaling / monocyte chemotaxis / positive regulation of translational initiation / 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 viral genome replication / cellular response to interleukin-1 / positive regulation of phosphorylation / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of T cell proliferation / 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 / intracellular calcium ion homeostasis / response to toxic substance / cellular response to virus / cellular response to type II interferon / : / calcium ion transport / chemotaxis / cell-cell signaling / cellular response to tumor necrosis factor / G alpha (i) signalling events / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / 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 | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å | |||||||||
Authors | Chen, Y.C. / Li, K.M. / Chen, P.J. / Zarivach, R. / Sun, Y.J. / Sue, S.C. | |||||||||
Funding support | Taiwan, 2items
| |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2020 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6aez.cif.gz | 100.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6aez.ent.gz | 76.3 KB | Display | PDB format |
PDBx/mmJSON format | 6aez.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ae/6aez ftp://data.pdbj.org/pub/pdb/validation_reports/ae/6aez | HTTPS FTP |
---|
-Related structure data
Related structure data | 5yamC 1eqtS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components on special symmetry positions |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Refine code: 0
NCS ensembles :
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | AUTHOR DETERMINED BIOLOGICAL ASSEMBLY: UNKNOWN. |
-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.) Homo sapiens (human) / Gene: CCL5, D17S136E, SCYA5 / Production host: Escherichia coli (E. coli) / References: UniProt: P13501 #2: Protein | | Mass: 7993.207 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CCL5, D17S136E, SCYA5 / Production host: Escherichia coli (E. coli) / References: UniProt: P13501 #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.3 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å |
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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.63→53.09 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|