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Yorodumi- PDB-1hig: THREE-DIMENSIONAL STRUCTURE OF RECOMBINANT HUMAN INTERFERON-GAMMA. -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hig | ||||||
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Title | THREE-DIMENSIONAL STRUCTURE OF RECOMBINANT HUMAN INTERFERON-GAMMA. | ||||||
Components | INTERFERON-GAMMA | ||||||
Keywords | GLYCOPROTEIN | ||||||
Function / homology | Function and homology information 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 cellular respiration ...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 cellular respiration / positive regulation of peptidyl-serine phosphorylation of STAT protein / positive regulation of interleukin-23 production / negative regulation of amyloid-beta clearance / positive regulation of calcidiol 1-monooxygenase activity / type III interferon-mediated signaling pathway / positive regulation of protein deacetylation / 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 MHC class II biosynthetic process / negative regulation of interleukin-17 production / positive regulation of osteoclast differentiation / regulation of metabolic process / positive regulation of signaling receptor activity / positive regulation of membrane protein ectodomain proteolysis / positive regulation of neurogenesis / negative regulation of epithelial cell differentiation / positive regulation of amyloid-beta formation / IFNG signaling activates MAPKs / positive regulation of epithelial cell migration / positive regulation of nitric-oxide synthase biosynthetic process / regulation of insulin secretion / cell surface receptor signaling pathway via JAK-STAT / macrophage differentiation / humoral immune response / type II interferon-mediated signaling pathway / positive regulation of autophagy / Regulation of IFNG signaling / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of phagocytosis / positive regulation of chemokine production / extrinsic apoptotic signaling pathway / positive regulation of interleukin-12 production / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / positive regulation of glycolytic process / positive regulation of interleukin-1 beta production / positive regulation of cytokine production / cytokine activity / astrocyte activation / positive regulation of protein localization to plasma membrane / negative regulation of smooth muscle cell proliferation / positive regulation of protein-containing complex assembly / microglial cell activation / response to virus / positive regulation of protein serine/threonine kinase activity / cellular response to virus / positive regulation of interleukin-6 production / positive regulation of protein import into nucleus / positive regulation of inflammatory response / positive regulation of tumor necrosis factor production / Interferon gamma signaling / positive regulation of nitric oxide biosynthetic process / defense response to virus / adaptive immune response / cell surface receptor signaling pathway / negative regulation of gene expression / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / positive regulation of gene expression / apoptotic process / negative regulation of transcription by RNA polymerase II / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 3.5 Å | ||||||
Authors | Ealick, S.E. / Cook, W.J. / Vijay-Kumar, S. / Carson, M. / Nagabhushan, T.L. / Trotta, P.P. / Bugg, C.E. | ||||||
Citation | Journal: Science / Year: 1991 Title: Three-dimensional structure of recombinant human interferon-gamma. Authors: Ealick, S.E. / Cook, W.J. / Vijay-Kumar, S. / Carson, M. / Nagabhushan, T.L. / Trotta, P.P. / Bugg, C.E. #1: Journal: J.Biol.Chem. / Year: 1987 Title: Crystallization and Preliminary X-Ray Investigation of a Recombinant Form of Human Gamma-Interferon Authors: Vijay-Kumar, S. / Senadhi, S.E. / Ealick, S.E. / Nagabhushan, T.L. / Trotta, P.P. / Kosecki, R. / Reichert, P. / Bugg, C.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hig.cif.gz | 25.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hig.ent.gz | 13.9 KB | Display | PDB format |
PDBx/mmJSON format | 1hig.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1hig_validation.pdf.gz | 319.5 KB | Display | wwPDB validaton report |
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Full document | 1hig_full_validation.pdf.gz | 319.5 KB | Display | |
Data in XML | 1hig_validation.xml.gz | 728 B | Display | |
Data in CIF | 1hig_validation.cif.gz | 4.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hi/1hig ftp://data.pdbj.org/pub/pdb/validation_reports/hi/1hig | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: RESIDUES 1, 2, 18 - 28, AND 121 - 123 FIT THE ELECTRON DENSITY POORLY. | ||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
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Details | THE TRANSFORMATION GIVEN ON THE FIRST SET OF *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *B* WHEN APPLIED TO CHAIN *A*. THIS CORRESPONDS TO A ROTATION ANGLE OF 179.8892 DEGREES ABOUT AN AXIS PARALLEL TO (0.6776,0.3150,-0.6646). THE TRANSFORMATION GIVEN ON THE SECOND SET OF *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *C* WHEN APPLIED TO CHAIN *A*. THIS CORRESPONDS TO A ROTATION ANGLE OF 179.9508 DEGREES ABOUT AN AXIS PARALLEL TO (0.1308,0.8370,0.5313). THE TRANSFORMATION GIVEN ON THE THIRD SET OF *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *D* WHEN APPLIED TO CHAIN *A*. THIS CORRESPONDS TO A ROTATION ANGLE OF 179.6269 DEGREES ABOUT AN AXIS PARALLEL TO (0.7199,-0.4474,0.5307). |
-Components
#1: Protein | Mass: 16205.518 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P01579 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.04 Å3/Da / Density % sol: 59.51 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 25 ℃ / pH: 5.9 / Method: vapor diffusion, hanging drop / Details: referred to J.Biol.Chem. 262.4804 1987 | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.8 Å / Num. obs: 19954 / Num. measured all: 158195 / Rmerge(I) obs: 0.113 |
-Processing
Software | Name: X-PLOR / Classification: refinement | ||||||||||||
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Refinement | Resolution: 3.5→6 Å /
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Refinement step | Cycle: LAST / Resolution: 3.5→6 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 6 Å / Num. reflection obs: 13192 / σ(I): 2 / Rfactor obs: 0.25 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS | ||||||||||||
Refine LS restraints | *PLUS
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