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Yorodumi- PDB-4p0l: Crystal Structure of Double Loop-Swapped Interleukin-36Ra With Ad... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4p0l | ||||||
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Title | Crystal Structure of Double Loop-Swapped Interleukin-36Ra With Additional Point Mutations | ||||||
Components | Interleukin-36 receptor antagonist/Interleukin-36 gamma chimera protein | ||||||
Keywords | CYTOKINE / chimera protein / interleukin | ||||||
Function / homology | Function and homology information interleukin-1 receptor antagonist activity / Interleukin-36 pathway / negative regulation of cytokine-mediated signaling pathway / antifungal humoral response / negative regulation of interleukin-17 production / interleukin-1 receptor binding / inflammatory response to antigenic stimulus / negative regulation of interleukin-6 production / negative regulation of type II interferon production / cytokine activity ...interleukin-1 receptor antagonist activity / Interleukin-36 pathway / negative regulation of cytokine-mediated signaling pathway / antifungal humoral response / negative regulation of interleukin-17 production / interleukin-1 receptor binding / inflammatory response to antigenic stimulus / negative regulation of interleukin-6 production / negative regulation of type II interferon production / cytokine activity / cytokine-mediated signaling pathway / cell-cell signaling / cellular response to lipopolysaccharide / innate immune response / positive regulation of gene expression / extracellular space / extracellular region / nucleoplasm / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 Å | ||||||
Authors | Guenther, S. / Sundberg, E.J. | ||||||
Funding support | United States, 1items
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Citation | Journal: J Immunol. / Year: 2014 Title: Molecular Determinants of Agonist and Antagonist Signaling through the IL-36 Receptor. Authors: Gunther, S. / Sundberg, E.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4p0l.cif.gz | 46.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4p0l.ent.gz | 30.6 KB | Display | PDB format |
PDBx/mmJSON format | 4p0l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4p0l_validation.pdf.gz | 422.8 KB | Display | wwPDB validaton report |
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Full document | 4p0l_full_validation.pdf.gz | 424.1 KB | Display | |
Data in XML | 4p0l_validation.xml.gz | 9 KB | Display | |
Data in CIF | 4p0l_validation.cif.gz | 12.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p0/4p0l ftp://data.pdbj.org/pub/pdb/validation_reports/p0/4p0l | HTTPS FTP |
-Related structure data
Related structure data | 4izeC 4p0jC 4p0kC 1md6S 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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Unit cell |
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-Components
#1: Protein | Mass: 16768.971 Da / Num. of mol.: 1 / Mutation: V2S, R107A, M109A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9UBH0, UniProt: Q9NZH8 |
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#2: 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: 1.89 Å3/Da / Density % sol: 34.8 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.3 / Details: 30% (w/v) PEG5000MME, 0.1 M NaAcetate, pH 5.3 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 6, 2013 |
Radiation | Monochromator: Si double crystal / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97945 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→37 Å / Num. obs: 19268 / % possible obs: 99.9 % / Redundancy: 9.5 % / Biso Wilson estimate: 17.12 Å2 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.022 / Net I/σ(I): 20.5 / Num. measured all: 183258 |
Reflection shell | Resolution: 1.55→1.58 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.735 / Mean I/σ(I) obs: 2.8 / Num. measured all: 8548 / Num. unique all: 913 / Rpim(I) all: 0.25 / Rejects: 0 / % possible all: 98.8 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1md6 Resolution: 1.55→37 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.58 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 79.64 Å2 / Biso mean: 23.6177 Å2 / Biso min: 9.91 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.55→37 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7 / % reflection obs: 100 %
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