+Open data
-Basic information
Entry | Database: PDB / ID: 3ona | ||||||
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Title | The SECRET domain in complex with CX3CL1 | ||||||
Components |
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Keywords | VIRAL PROTEIN/CYTOKINE / beta-sandwich / chemokine fold / vTNFR-chemokine complex / VIRAL PROTEIN-CYTOKINE complex | ||||||
Function / homology | Function and homology information 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 / tumor necrosis factor receptor activity / synapse pruning ...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 / tumor necrosis factor receptor activity / 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 / integrin activation / 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 / 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 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 / 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 | Ectromelia virus Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Wang, X.Q. / Xue, X.G. / Wang, D.L. | ||||||
Citation | Journal: Plos Pathog. / Year: 2011 Title: Structural basis of chemokine sequestration by CrmD, a poxvirus-encoded tumor necrosis factor receptor Authors: Xue, X.G. / Lu, Q.Y. / Wei, H. / Wang, D.L. / Chen, D.W. / He, G.J. / Huang, L. / Wang, H.Z. / Wang, X.Q. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ona.cif.gz | 103 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ona.ent.gz | 79.5 KB | Display | PDB format |
PDBx/mmJSON format | 3ona.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ona_validation.pdf.gz | 434.5 KB | Display | wwPDB validaton report |
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Full document | 3ona_full_validation.pdf.gz | 441.3 KB | Display | |
Data in XML | 3ona_validation.xml.gz | 11.2 KB | Display | |
Data in CIF | 3ona_validation.cif.gz | 14.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/on/3ona ftp://data.pdbj.org/pub/pdb/validation_reports/on/3ona | HTTPS FTP |
-Related structure data
Related structure data | 3on9SC 1f2lS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 18012.010 Da / Num. of mol.: 1 / Fragment: SECRET domain, UNP residues 162-320 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ectromelia virus / Gene: crmD / Production host: Escherichia coli (E. coli) / References: UniProt: Q7TDW8 |
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#2: Protein | Mass: 8971.408 Da / Num. of mol.: 1 / Fragment: chemokine domain, UNP residues 24-100 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q6I9S9, UniProt: P78423*PLUS |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.48 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.2M Li2SO4, 0.1M Tris.Cl, 20% PEG 4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 6, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. all: 8839 / Num. obs: 8847 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.6→2.69 Å / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 3ON9 AND 1F2L Resolution: 2.6→29.317 Å / SU ML: 1.79 / σ(F): 0.06 / 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 / Bsol: 72.036 Å2 / ksol: 0.354 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.6→29.317 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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