+Open data
-Basic information
Entry | Database: PDB / ID: 1u4r | ||||||
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Title | Crystal Structure of human RANTES mutant 44-AANA-47 | ||||||
Components | Small inducible cytokine A5 | ||||||
Keywords | ATTRACTANT / CHEMOATTRACTANT / CYTOKINE / CHEMOKINE / RANTES / MUTANT / GLYCOSAMINOGLYCAN / PROTEIN-HEPARIN DISACCHARIDE COMPLEX | ||||||
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 / 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 / positive regulation of calcium ion transport / neutrophil activation / 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 / positive regulation of macrophage chemotaxis / phospholipase activator activity / 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 / cellular response to interleukin-1 / positive regulation of viral genome replication / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Shaw, J.P. / Johnson, Z. / Borlat, F. / Zwahlen, C. / Kungl, A. / Roulin, K. / Harrenga, A. / Wells, T.N.C. / Proudfoot, A.E.I. | ||||||
Citation | Journal: Structure / Year: 2004 Title: The X-ray structure of RANTES: heparin-derived disaccharides allows the rational design of chemokine inhibitors. Authors: Shaw, J.P. / Johnson, Z. / Borlat, F. / Zwahlen, C. / Kungl, A. / Roulin, K. / Harrenga, A. / Wells, T.N. / Proudfoot, A.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1u4r.cif.gz | 67.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1u4r.ent.gz | 49.8 KB | Display | PDB format |
PDBx/mmJSON format | 1u4r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u4/1u4r ftp://data.pdbj.org/pub/pdb/validation_reports/u4/1u4r | HTTPS FTP |
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-Related structure data
Related structure data | 1u4lC 1u4mC 1u4pSC C: citing same article (ref.) S: Starting model for refinement |
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Similar 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
#1: Protein | Mass: 7631.676 Da / Num. of mol.: 4 / Mutation: R44A, K45A, R47A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CCL5, SCYA5 / Plasmid: pET23d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P13501 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 33.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: 25% PEG 400, 100mM acetate buffer, 200mM (NH4)2SO4, 10% (v/v) glycerol, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: AREA DETECTOR / Date: Jun 12, 2002 / Details: mirrors |
Radiation | Monochromator: Osmic MaxFlux Confocal Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. obs: 11304 / % possible obs: 93.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 2.9 % / Biso Wilson estimate: 19 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 2.2→2.28 Å / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.9 / Num. unique all: 917 / % possible all: 75 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1u4p Resolution: 2.2→15.63 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 957758.91 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: BABINET / Bsol: 280 Å2 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→15.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
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Xplor file |
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