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Yorodumi- PDB-1fyh: 1:1 COMPLEX BETWEEN AN INTERFERON GAMMA SINGLE-CHAIN VARIANT AND ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fyh | ||||||
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Title | 1:1 COMPLEX BETWEEN AN INTERFERON GAMMA SINGLE-CHAIN VARIANT AND ITS RECEPTOR | ||||||
Components |
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Keywords | IMMUNE SYSTEM / CYTOKINE-RECEPTOR COMPLEX / FIBRONECTIN TYPE-III | ||||||
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 / 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 / negative regulation of gene expression / negative regulation of DNA-templated transcription / apoptotic process / positive regulation of cell population proliferation / positive regulation of gene expression / negative regulation of transcription by RNA polymerase II / signal transduction / extracellular space / extracellular region / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.04 Å | ||||||
Authors | Randal, M. / Kossiakoff, A.A. | ||||||
Citation | Journal: Structure / Year: 2001 Title: The structure and activity of a monomeric interferon-gamma:alpha-chain receptor signaling complex. Authors: Randal, M. / Kossiakoff, A.A. #1: Journal: Protein Sci. / Year: 1998 Title: Crystallization and Preliminary X-ray Analysis of a 1:1 Complex between a designed monomeric interferon-gamma and it soluble receptor Authors: Randal, M. / Kossiakoff, A.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fyh.cif.gz | 195.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fyh.ent.gz | 162.4 KB | Display | PDB format |
PDBx/mmJSON format | 1fyh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fy/1fyh ftp://data.pdbj.org/pub/pdb/validation_reports/fy/1fyh | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | the biological assembly consists of one single-chain interferon gamma and one receptor |
-Components
#1: Protein | Mass: 30146.277 Da / Num. of mol.: 2 / Fragment: UNP residues 24-143, 28-156 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IFNG / Plasmid: PRSET / Production host: Escherichia coli (E. coli) / References: UniProt: P01579 #2: Protein | Mass: 25900.158 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAIN (UNP residues 18-246) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: IFNGR1 / Plasmid: PAP / Production host: Escherichia coli (E. coli) / References: UniProt: P15260 #3: Chemical | ChemComp-CL / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.95 Å3/Da / Density % sol: 58.29 % | ||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: ammonium sulphate, PEG 8000, Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||
Crystal | *PLUS Density % sol: 55 % | ||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.91 |
Detector | Type: ADSC / Detector: CCD / Date: May 16, 1995 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91 Å / Relative weight: 1 |
Reflection | Resolution: 2.04→15 Å / Num. all: 79612 / Num. obs: 79612 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.6 % / Biso Wilson estimate: 26.1 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 2.04→2.11 Å / Rmerge(I) obs: 0.209 / Num. unique all: 6674 / % possible all: 81.1 |
Reflection | *PLUS Num. obs: 80837 / % possible obs: 956.9 % / Num. measured all: 773440 |
Reflection shell | *PLUS % possible obs: 86.5 % |
-Processing
Software |
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Refinement | Resolution: 2.04→15 Å / Rfactor Rfree error: 0.003 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 35.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.04→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.04→2.11 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 10
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Xplor file | Serial no: 1 / Param file: parhcsdx.pro / Topol file: tophcsdx.pro | ||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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