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Yorodumi- PDB-1y6n: Crystal structure of Epstein-Barr virus IL-10 mutant (A87I) compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1y6n | ||||||
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Title | Crystal structure of Epstein-Barr virus IL-10 mutant (A87I) complexed with the soluble IL-10R1 chain | ||||||
Components |
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Keywords | IMMUNE SYSTEM / HELIX BUNDLE / RECEPTOR COMPLEX | ||||||
Function / homology | Function and homology information interleukin-10 binding / interleukin-10 receptor activity / ubiquitin-dependent endocytosis / intestinal epithelial structure maintenance / regulation of synapse organization / Interleukin-10 signaling / regulation of cytokine production / negative regulation of autophagy / virus-mediated perturbation of host defense response / cytokine activity ...interleukin-10 binding / interleukin-10 receptor activity / ubiquitin-dependent endocytosis / intestinal epithelial structure maintenance / regulation of synapse organization / Interleukin-10 signaling / regulation of cytokine production / negative regulation of autophagy / virus-mediated perturbation of host defense response / cytokine activity / positive regulation of receptor signaling pathway via JAK-STAT / negative regulation of inflammatory response / cytokine-mediated signaling pathway / signaling receptor activity / response to lipopolysaccharide / immune response / apical plasma membrane / extracellular space / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Human herpesvirus 4 (Epstein-Barr virus) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å | ||||||
Authors | Yoon, S.I. / Jones, B.C. / Logsdon, N.J. / Walter, M.R. | ||||||
Citation | Journal: Structure / Year: 2005 Title: Same structure, different function crystal structure of the Epstein-Barr virus IL-10 bound to the soluble IL-10R1 chain. Authors: Yoon, S.I. / Jones, B.C. / Logsdon, N.J. / Walter, M.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1y6n.cif.gz | 80.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1y6n.ent.gz | 64.1 KB | Display | PDB format |
PDBx/mmJSON format | 1y6n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y6/1y6n ftp://data.pdbj.org/pub/pdb/validation_reports/y6/1y6n | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The second part of the biological assembly is generated by the two fold axis: x, x-y, -z. |
-Components
#1: Protein | Mass: 17439.266 Da / Num. of mol.: 1 / Fragment: residues 26-170 / Mutation: A87I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human herpesvirus 4 (Epstein-Barr virus) Genus: Lymphocryptovirus / Strain: GD1 / Gene: BCRF1 / Plasmid: pET-32 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 (DE3) / References: UniProt: P03180 |
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#2: Protein | Mass: 24506.551 Da / Num. of mol.: 1 / Fragment: Extracellular domain, residues 22-235 / Mutation: N29Q, N53Q, N89Q, N133Q, N156Q, N168Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IL10RA, IL10R / Plasmid: pMTV5HIS / Cell line (production host): SCHNEIDER CELLS / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q13651 |
#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: 2.2 Å3/Da / Density % sol: 45 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: PEG 6000, magnesium chloride, ADA, MPD, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9252, 0.9794 | |||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD | |||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.7→60 Å / Num. all: 10500 / Num. obs: 10500 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 57 Å2 / Rmerge(I) obs: 0.059 | |||||||||
Reflection shell | Resolution: 2.7→2.8 Å / Rmerge(I) obs: 0.245 / % possible all: 85.1 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.7→25 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refine analyze | Luzzati coordinate error free: 0.43 Å | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.8 Å
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