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Yorodumi- PDB-7pur: mouse Interleukin-12 subunit beta - p80 homodimer in space group ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7pur | ||||||
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Title | mouse Interleukin-12 subunit beta - p80 homodimer in space group P21 crystal form 2 | ||||||
Components | Interleukin-12 subunit beta | ||||||
Keywords | CYTOKINE / interleukin / homodimer | ||||||
Function / homology | Function and homology information Interleukin-12 signaling / Interleukin-23 signaling / interleukin-23 receptor binding / interleukin-12 alpha subunit binding / interleukin-12 complex / interleukin-23 complex / natural killer cell activation involved in immune response / positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / negative regulation of vascular endothelial growth factor signaling pathway / negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis ...Interleukin-12 signaling / Interleukin-23 signaling / interleukin-23 receptor binding / interleukin-12 alpha subunit binding / interleukin-12 complex / interleukin-23 complex / natural killer cell activation involved in immune response / positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / negative regulation of vascular endothelial growth factor signaling pathway / negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis / positive regulation of T-helper 1 type immune response / positive regulation of smooth muscle cell apoptotic process / natural killer cell activation / T-helper cell differentiation / positive regulation of osteoclast differentiation / negative regulation of interleukin-17 production / positive regulation of NK T cell proliferation / interleukin-12-mediated signaling pathway / response to UV-B / positive regulation of natural killer cell proliferation / positive regulation of granulocyte macrophage colony-stimulating factor production / cytokine receptor activity / negative regulation of interleukin-10 production / positive regulation of activated T cell proliferation / defense response to protozoan / positive regulation of interleukin-17 production / positive regulation of interleukin-10 production / immunoglobulin mediated immune response / negative regulation of protein secretion / T cell proliferation / positive regulation of T cell proliferation / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of defense response to virus by host / negative regulation of inflammatory response to antigenic stimulus / positive regulation of interleukin-12 production / : / cytokine activity / endosome lumen / negative regulation of smooth muscle cell proliferation / growth factor activity / cytokine-mediated signaling pathway / cellular response to type II interferon / Golgi lumen / positive regulation of T cell mediated cytotoxicity / positive regulation of tumor necrosis factor production / positive regulation of type II interferon production / cell migration / cellular response to lipopolysaccharide / defense response to Gram-negative bacterium / defense response to virus / cell population proliferation / cell surface receptor signaling pathway / protein heterodimerization activity / endoplasmic reticulum lumen / external side of plasma membrane / protein-containing complex binding / cell surface / extracellular space / extracellular region / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.9 Å | ||||||
Authors | Bloch, Y. / Savvides, S.N. | ||||||
Funding support | Belgium, 1items
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Citation | Journal: To Be Published Title: Around she goes: the structure of mouse Interleukin-12 p80 Authors: Bloch, Y. / Savvides, S.N. #1: Journal: Acta Crystallogr D Struct Biol / Year: 2020 Title: Homogeneously N-glycosylated proteins derived from the GlycoDelete HEK293 cell line enable diffraction-quality crystallogenesis. Authors: Kozak, S. / Bloch, Y. / De Munck, S. / Mikula, A. / Bento, I. / Savvides, S.N. / Meijers, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7pur.cif.gz | 283.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7pur.ent.gz | 207.1 KB | Display | PDB format |
PDBx/mmJSON format | 7pur.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7pur_validation.pdf.gz | 1004.2 KB | Display | wwPDB validaton report |
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Full document | 7pur_full_validation.pdf.gz | 1005.2 KB | Display | |
Data in XML | 7pur_validation.xml.gz | 22.7 KB | Display | |
Data in CIF | 7pur_validation.cif.gz | 30.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pu/7pur ftp://data.pdbj.org/pub/pdb/validation_reports/pu/7pur | HTTPS FTP |
-Related structure data
Related structure data | 6smcC 6sp3C 7r3nC 6sffS 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
#1: Protein | Mass: 39398.594 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: First 22 aminoacids are part of the secretion signal and are likely removed during translocation to the ER. Source: (gene. exp.) Mus musculus (house mouse) / Gene: Il12b / Plasmid: pHLsec / Cell line (production host): HEK293S Glycodelete / Production host: Homo sapiens (human) / References: UniProt: P43432 #2: Polysaccharide | alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #3: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.93 % |
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Crystal grow | Temperature: 287 K / Method: vapor diffusion, sitting drop / Details: 5% MPD, 10% PEG6000, 100mM TRIS pH7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 26, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 3.88→79.18 Å / Num. obs: 7714 / % possible obs: 97.8 % / Redundancy: 3.13 % / Biso Wilson estimate: 117.65 Å2 / CC1/2: 0.978 / Rrim(I) all: 0.325 / Net I/σ(I): 4.79 |
Reflection shell | Resolution: 3.88→4.11 Å / Redundancy: 3.13 % / Mean I/σ(I) obs: 0.87 / Num. unique obs: 1182 / CC1/2: 0.375 / Rrim(I) all: 1.9 / % possible all: 93 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6sff Resolution: 3.9→39.62 Å / SU ML: 0.8238 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 37.9693 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 137.3 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.9→39.62 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 | Refine-ID: X-RAY DIFFRACTION
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