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- PDB-4zlt: Crystal structure of viral chemokine binding protein R17 in compl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4zlt | |||||||||||||||
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Title | Crystal structure of viral chemokine binding protein R17 in complex with CCL3 | |||||||||||||||
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![]() | Chemokine binding protein/Chemokine / RHVP chemokine binding protein in complex with chemokine CCL3 / Chemokine binding protein-Chemokine complex | |||||||||||||||
Function / homology | ![]() Chemokine receptors bind chemokines / calcium,diacylglycerol-dependent serine/threonine kinase activity / granulocyte chemotaxis / positive regulation of natural killer cell chemotaxis / signaling / astrocyte cell migration / response to xenobiotic stimulus => GO:0009410 / eosinophil degranulation / regulation of sensory perception of pain / CCR chemokine receptor binding ...Chemokine receptors bind chemokines / calcium,diacylglycerol-dependent serine/threonine kinase activity / granulocyte chemotaxis / positive regulation of natural killer cell chemotaxis / signaling / astrocyte cell migration / response to xenobiotic stimulus => GO:0009410 / eosinophil degranulation / regulation of sensory perception of pain / CCR chemokine receptor binding / lymphocyte chemotaxis / cell activation / T cell chemotaxis / positive regulation of calcium ion transport / eosinophil chemotaxis / positive regulation of osteoclast differentiation / response to cholesterol / chemokine-mediated signaling pathway / leukocyte chemotaxis / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / chemokine activity / phospholipase activator activity / exocytosis / chemoattractant activity / negative regulation of osteoclast differentiation / macrophage chemotaxis / monocyte chemotaxis / cellular response to organic cyclic compound / negative regulation by host of viral transcription / cellular response to interleukin-1 / positive regulation of calcium-mediated signaling / lipopolysaccharide-mediated signaling pathway / cytoskeleton organization / phosphatidylinositol 3-kinase/protein kinase B signal transduction / neutrophil chemotaxis / positive regulation of GTPase activity / positive regulation of interleukin-1 beta production / calcium-mediated signaling / response to toxic substance / cellular response to type II interferon / intracellular calcium ion homeostasis / positive regulation of inflammatory response / osteoblast differentiation / calcium ion transport / chemotaxis / positive regulation of tumor necrosis factor production / MAPK cascade / positive regulation of neuron apoptotic process / cell-cell signaling / kinase activity / cellular response to tumor necrosis factor / regulation of cell shape / positive regulation of cytosolic calcium ion concentration / positive regulation of ERK1 and ERK2 cascade / protein kinase activity / positive regulation of cell migration / inflammatory response / G protein-coupled receptor signaling pathway / protein phosphorylation / negative regulation of gene expression / positive regulation of gene expression / positive regulation of transcription by RNA polymerase II / extracellular space / cytoplasm / cytosol Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() ![]() | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Lubman, O.Y. / Fremont, D.H. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Parallel Evolution of Chemokine Binding by Structurally Related Herpesvirus Decoy Receptors. Authors: Lubman, O.Y. / Fremont, D.H. | |||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 187.5 KB | Display | ![]() |
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PDB format | ![]() | 148.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 484.6 KB | Display | ![]() |
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Full document | ![]() | 505.5 KB | Display | |
Data in XML | ![]() | 34 KB | Display | |
Data in CIF | ![]() | 45.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4zkqSC ![]() 2x6gS 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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2 | ![]()
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Unit cell |
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Details | dimer according to multi-angle static light scattering |
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Components
#1: Protein | Mass: 47388.625 Da / Num. of mol.: 2 / Mutation: K333D, R335E, R336E, K337D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() #2: Protein | Mass: 7982.065 Da / Num. of mol.: 2 / Mutation: D27A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Sugar | ChemComp-NAG / |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.1 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / Details: 15-20% PEG 3350 0.2-0.4M MgFormate |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||
Detector | Type: NOIR-1 / Detector: CCD / Date: Jun 13, 2013 | |||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||
Reflection | Resolution: 2.761→50 Å / Num. obs: 26825 / % possible obs: 100 % / Redundancy: 4.7 % / Rsym value: 0.11 / Net I/σ(I): 7.4 | |||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4ZKQ and 2X6G Resolution: 3→49.247 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 27.94 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→49.247 Å
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Refine LS restraints |
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LS refinement shell |
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