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Open data
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Basic information
Entry | Database: PDB / ID: 4xt3 | |||||||||
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Title | Structure of a viral GPCR bound to human chemokine CX3CL1 | |||||||||
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![]() | VIRAL PROTEIN/SIGNALLING PROTEIN / GPCR / chemokine / membrane protein / complex / VIRAL PROTEIN-CYTOKINE complex / VIRAL PROTEIN-SIGNALLING PROTEIN complex | |||||||||
Function / homology | ![]() positive regulation by virus of host cell division / CXCR1 chemokine receptor binding / positive regulation of calcium-independent cell-cell adhesion / negative regulation of glutamate receptor signaling pathway / negative regulation of interleukin-1 alpha production / leukocyte adhesive activation / CX3C chemokine receptor binding / negative regulation of hippocampal neuron apoptotic process / autocrine signaling / synapse pruning ...positive regulation by virus of host cell division / CXCR1 chemokine receptor binding / positive regulation of calcium-independent cell-cell adhesion / negative regulation of glutamate receptor signaling pathway / negative regulation of interleukin-1 alpha production / leukocyte adhesive activation / CX3C chemokine receptor binding / negative regulation of hippocampal neuron apoptotic process / autocrine signaling / synapse pruning / negative regulation of neuron migration / positive regulation of microglial cell migration / negative regulation of microglial cell activation / regulation of lipopolysaccharide-mediated signaling pathway / positive regulation of transforming growth factor beta1 production / positive regulation of I-kappaB phosphorylation / microglial cell proliferation / CCR chemokine receptor binding / positive regulation of actin filament bundle assembly / lymphocyte chemotaxis / leukocyte migration involved in inflammatory response / C-C chemokine receptor activity / integrin activation / C-C chemokine binding / angiogenesis involved in wound healing / eosinophil chemotaxis / chemokine-mediated signaling pathway / leukocyte chemotaxis / Chemokine receptors bind chemokines / chemokine activity / negative regulation of cell-substrate adhesion / negative regulation of interleukin-1 beta production / positive regulation of cell-matrix adhesion / neuron remodeling / positive regulation of neuroblast proliferation / positive chemotaxis / chemoattractant activity / monocyte chemotaxis / negative regulation of interleukin-6 production / negative regulation of apoptotic signaling pathway / negative regulation of tumor necrosis factor production / regulation of neurogenesis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / cellular response to interleukin-1 / extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of cell migration / neutrophil chemotaxis / cell chemotaxis / positive regulation of release of sequestered calcium ion into cytosol / cell projection / response to ischemia / calcium-mediated signaling / positive regulation of smooth muscle cell proliferation / microglial cell activation / regulation of synaptic plasticity / defense response / cytokine-mediated signaling pathway / positive regulation of neuron projection development / cellular response to type II interferon / cell-cell adhesion / neuron cellular homeostasis / positive regulation of inflammatory response / chemotaxis / integrin binding / cell-cell signaling / cellular response to tumor necrosis factor / G alpha (i) signalling events / positive regulation of cytosolic calcium ion concentration / positive regulation of canonical NF-kappaB signal transduction / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / cell adhesion / inflammatory response / neuron projection / immune response / G protein-coupled receptor signaling pathway / signaling receptor binding / virus-mediated perturbation of host defense response / neuronal cell body / positive regulation of cell population proliferation / negative regulation of apoptotic process / host cell plasma membrane / perinuclear region of cytoplasm / cell surface / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Burg, J.S. / Jude, K.M. / Waghray, D. / Garcia, K.C. | |||||||||
![]() | ![]() Title: Structural biology. Structural basis for chemokine recognition and activation of a viral G protein-coupled receptor. Authors: Burg, J.S. / Ingram, J.R. / Venkatakrishnan, A.J. / Jude, K.M. / Dukkipati, A. / Feinberg, E.N. / Angelini, A. / Waghray, D. / Dror, R.O. / Ploegh, H.L. / Garcia, K.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 | ![]() | 89.1 KB | Display | ![]() |
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PDB format | ![]() | 63 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 739.5 KB | Display | ![]() |
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Full document | ![]() | 742.7 KB | Display | |
Data in XML | ![]() | 14.9 KB | Display | |
Data in CIF | ![]() | 19.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4xt1C ![]() 1f2lS ![]() 3onaS ![]() 4mbsS C: citing same article ( S: Starting model for refinement |
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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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Components
#1: Protein | Mass: 42041.098 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Protein | Mass: 10013.487 Da / Num. of mol.: 1 / Fragment: UNP residues 25-101 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / triacetyl-beta-chitotriose |
#4: Chemical | ChemComp-UNL / Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#5: Chemical | ChemComp-PO4 / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 52.99 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 7.4 / Details: PEG 300, HEPES, ammonium phosphate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PILATUS3 6M / Detector: PIXEL / Date: Apr 20, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 3.8→48.92 Å / Num. obs: 4834 / % possible obs: 85 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.275 / Net I/σ(I): 4.1 |
Reflection shell | Resolution: 3.8→3.937 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.555 / Mean I/σ(I) obs: 1.6 / % possible all: 55.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4MBS, 1F2L, 3ONA Resolution: 3.801→48.92 Å / SU ML: 0.66 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 39.58 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.801→48.92 Å
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Refine LS restraints |
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LS refinement shell |
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