[English] 日本語
![](img/lk-miru.gif)
- PDB-1fyh: 1:1 COMPLEX BETWEEN AN INTERFERON GAMMA SINGLE-CHAIN VARIANT AND ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1fyh | ||||||
---|---|---|---|---|---|---|---|
Title | 1:1 COMPLEX BETWEEN AN INTERFERON GAMMA SINGLE-CHAIN VARIANT AND ITS RECEPTOR | ||||||
![]() |
| ||||||
![]() | IMMUNE SYSTEM / CYTOKINE-RECEPTOR COMPLEX / FIBRONECTIN TYPE-III | ||||||
Function / homology | ![]() 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 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 / positive regulation of protein deacetylation / 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 / Regulation of IFNG signaling / type II interferon-mediated signaling pathway / extrinsic apoptotic signaling pathway / positive regulation of chemokine production / positive regulation of phagocytosis / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of interleukin-12 production / positive regulation of glycolytic process / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / 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 / microglial cell activation / positive regulation of protein-containing complex assembly / response to virus / positive regulation of protein serine/threonine kinase activity / cellular response to virus / cytokine-mediated signaling pathway / positive regulation of protein import into nucleus / positive regulation of inflammatory response / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / Interferon gamma signaling / positive regulation of nitric oxide biosynthetic process / 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 | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Randal, M. / Kossiakoff, A.A. | ||||||
![]() | ![]() Title: The structure and activity of a monomeric interferon-gamma:alpha-chain receptor signaling complex. Authors: Randal, M. / Kossiakoff, A.A. #1: ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 195.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 162.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 390.9 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 400.7 KB | Display | |
Data in XML | ![]() | 17.8 KB | Display | |
Data in CIF | ![]() | 30.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
| ||||||||
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.) ![]() ![]() ![]() #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.) ![]() ![]() ![]() #3: Chemical | ChemComp-CL / | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.95 Å3/Da / Density % sol: 58.29 % | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
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 |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
| ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.8 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.04→15 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.04→2.11 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 10
| ||||||||||||||||||||||||||||||||||||
Xplor file | Serial no: 1 / Param file: parhcsdx.pro / Topol file: tophcsdx.pro | ||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|