+Open data
-Basic information
Entry | Database: PDB / ID: 6e3k | |||||||||
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Title | Interferon gamma signalling complex with IFNGR1 and IFNGR2 | |||||||||
Components |
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Keywords | CYTOKINE / cytokine receptor / protein complex / protein engineering | |||||||||
Function / homology | Function and homology information type II interferon receptor activity / positive regulation of fructose 1,6-bisphosphate metabolic process / positive regulation of fructose 1,6-bisphosphate 1-phosphatase activity / positive regulation of tumor necrosis factor (ligand) superfamily member 11 production / positive regulation of iron ion import across plasma membrane / type II interferon receptor binding / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation involved in immune response / negative regulation of tau-protein kinase activity / positive regulation of NMDA glutamate receptor activity / : ...type II interferon receptor activity / positive regulation of fructose 1,6-bisphosphate metabolic process / positive regulation of fructose 1,6-bisphosphate 1-phosphatase activity / positive regulation of tumor necrosis factor (ligand) superfamily member 11 production / positive regulation of iron ion import across plasma membrane / type II interferon receptor binding / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation involved in immune response / negative regulation of tau-protein kinase activity / positive regulation of NMDA glutamate receptor activity / : / positive regulation of vitamin D biosynthetic process / positive regulation of peptidyl-serine phosphorylation of STAT protein / positive regulation of interleukin-23 production / negative regulation of amyloid-beta clearance / positive regulation of cellular respiration / positive regulation of protein deacetylation / positive regulation of calcidiol 1-monooxygenase activity / type III interferon-mediated signaling pathway / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / positive regulation of smooth muscle cell apoptotic process / positive regulation of core promoter binding / neuroinflammatory response / positive regulation of exosomal secretion / positive regulation of killing of cells of another organism / macrophage activation involved in immune response / positive regulation of osteoclast differentiation / positive regulation of MHC class II biosynthetic process / negative regulation of interleukin-17 production / positive regulation of signaling receptor activity / positive regulation of membrane protein ectodomain proteolysis / positive regulation of neurogenesis / cytokine receptor activity / negative regulation of epithelial cell differentiation / positive regulation of amyloid-beta formation / IFNG signaling activates MAPKs / positive regulation of epithelial cell migration / cytokine binding / positive regulation of nitric-oxide synthase biosynthetic process / cell surface receptor signaling pathway via JAK-STAT / regulation of insulin secretion / humoral immune response / macrophage differentiation / positive regulation of autophagy / type II interferon-mediated signaling pathway / Regulation of IFNG signaling / extrinsic apoptotic signaling pathway / positive regulation of phagocytosis / positive regulation of chemokine production / positive regulation of tyrosine phosphorylation of STAT protein / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / positive regulation of interleukin-12 production / positive regulation of glycolytic process / positive regulation of interleukin-1 beta production / positive regulation of cytokine production / cytokine activity / astrocyte activation / negative regulation of smooth muscle cell proliferation / positive regulation of protein localization to plasma membrane / microglial cell activation / response to virus / positive regulation of protein-containing complex assembly / cytoplasmic vesicle membrane / positive regulation of protein serine/threonine kinase activity / cellular response to virus / cytokine-mediated signaling pathway / positive regulation of inflammatory response / positive regulation of protein import into nucleus / positive regulation of interleukin-6 production / positive regulation of nitric oxide biosynthetic process / positive regulation of tumor necrosis factor production / Interferon gamma signaling / defense response to virus / adaptive immune response / Potential therapeutics for SARS / cell surface receptor signaling pathway / Golgi membrane / negative regulation of gene expression / negative regulation of DNA-templated transcription / apoptotic process / positive regulation of cell population proliferation / endoplasmic reticulum membrane / positive regulation of gene expression / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / signal transduction / extracellular space / extracellular region / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å | |||||||||
Authors | Jude, K.M. / Mendoza, J.L. / Garcia, K.C. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Nature / Year: 2019 Title: Structure of the IFN gamma receptor complex guides design of biased agonists. Authors: Mendoza, J.L. / Escalante, N.K. / Jude, K.M. / Sotolongo Bellon, J. / Su, L. / Horton, T.M. / Tsutsumi, N. / Berardinelli, S.J. / Haltiwanger, R.S. / Piehler, J. / Engleman, E.G. / Garcia, K.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6e3k.cif.gz | 473.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6e3k.ent.gz | 391.3 KB | Display | PDB format |
PDBx/mmJSON format | 6e3k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e3/6e3k ftp://data.pdbj.org/pub/pdb/validation_reports/e3/6e3k | HTTPS FTP |
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-Related structure data
Related structure data | 6e3lC 1fg9S 5eh1S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.15785/SBGRID/591 / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 17216.453 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IFNG / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P01579 |
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-Interferon gamma receptor ... , 2 types, 4 molecules CDEI
#2: Protein | Mass: 27363.729 Da / Num. of mol.: 2 / Mutation: T149I, M161K, Q167K, K174N, Q182R, H205N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IFNGR1 / Cell line (production host): HEK 293 / Production host: Homo sapiens (human) / References: UniProt: P15260 #3: Protein | Mass: 26310.582 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IFNGR2, IFNGT1 / Cell line (production host): HEK 293 / Production host: Homo sapiens (human) / References: UniProt: P38484 |
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-Sugars , 3 types, 14 molecules
#4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose |
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#5: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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 |
#6: Sugar | ChemComp-NAG / |
-Non-polymers , 3 types, 16 molecules
#7: Chemical | ChemComp-EDO / #8: Chemical | #9: Water | ChemComp-HOH / | |
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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: 4.42 Å3/Da / Density % sol: 72.16 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7 / Details: 100 mM Bis Tris Propane pH 7.0, 2 M sodium formate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 23, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 3.25→49.49 Å / Num. obs: 40393 / % possible obs: 99.9 % / Redundancy: 6.6 % / CC1/2: 0.994 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.058 / Rrim(I) all: 0.149 / Χ2: 0.88 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 3.25→3.38 Å / Redundancy: 6.8 % / Rmerge(I) obs: 1.454 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4469 / CC1/2: 0.7 / Rpim(I) all: 0.594 / Rrim(I) all: 1.573 / Χ2: 0.87 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1fg9, 5eh1 Resolution: 3.25→37.188 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.28
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.25→37.188 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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