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- PDB-1fg9: 3:1 COMPLEX OF INTERFERON-GAMMA RECEPTOR WITH INTERFERON-GAMMA DIMER -

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Basic information

Entry
Database: PDB / ID: 1fg9
Title3:1 COMPLEX OF INTERFERON-GAMMA RECEPTOR WITH INTERFERON-GAMMA DIMER
Components
  • INTERFERON GAMMA
  • INTERFERON-GAMMA RECEPTOR ALPHA CHAIN
KeywordsIMMUNE SYSTEM / cytokine-receptor complex / fibronectin type-III
Function / homology
Function and homology information


type II interferon receptor activity / : / : / positive regulation of peptidyl-serine phosphorylation of STAT protein / positive regulation of fructose 1,6-bisphosphate metabolic process / positive regulation of tumor necrosis factor (ligand) superfamily member 11 production / type II interferon receptor binding / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation involved in immune response / positive regulation of protein deacetylation / positive regulation of vitamin D biosynthetic process ...type II interferon receptor activity / : / : / positive regulation of peptidyl-serine phosphorylation of STAT protein / positive regulation of fructose 1,6-bisphosphate metabolic process / positive regulation of tumor necrosis factor (ligand) superfamily member 11 production / type II interferon receptor binding / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation involved in immune response / positive regulation of protein deacetylation / positive regulation of vitamin D biosynthetic process / positive regulation of cellular respiration / positive regulation of iron ion import across plasma membrane / positive regulation of interleukin-23 production / positive regulation of smooth muscle cell apoptotic process / type III interferon-mediated signaling pathway / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / negative regulation of amyloid-beta clearance / positive regulation of core promoter binding / neuroinflammatory response / positive regulation of exosomal secretion / positive regulation of glutamate receptor signaling pathway / positive regulation of MHC class II biosynthetic process / macrophage activation involved in immune response / negative regulation of interleukin-17 production / positive regulation of osteoclast differentiation / cytokine receptor activity / cell surface receptor signaling pathway via STAT / positive regulation of membrane protein ectodomain proteolysis / positive regulation of neurogenesis / regulation of metabolic process / positive regulation of tyrosine phosphorylation of STAT protein / IFNG signaling activates MAPKs / positive regulation of amyloid-beta formation / negative regulation of epithelial cell differentiation / cytokine binding / Fc-gamma receptor signaling pathway involved in phagocytosis / humoral immune response / macrophage differentiation / positive regulation of epithelial cell migration / positive regulation of protein serine/threonine kinase activity / cell surface receptor signaling pathway via JAK-STAT / type II interferon-mediated signaling pathway / Regulation of IFNG signaling / positive regulation of chemokine production / extrinsic apoptotic signaling pathway / positive regulation of interleukin-12 production / positive regulation of autophagy / astrocyte activation / regulation of insulin secretion / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / positive regulation of phagocytosis / positive regulation of glycolytic process / positive regulation of cytokine production / positive regulation of interleukin-1 beta production / cytokine activity / positive regulation of protein localization to plasma membrane / positive regulation of protein-containing complex assembly / negative regulation of smooth muscle cell proliferation / microglial cell activation / cellular response to virus / positive regulation of interleukin-6 production / positive regulation of protein import into nucleus / response to virus / cytokine-mediated signaling pathway / Interferon gamma signaling / positive regulation of inflammatory response / positive regulation of nitric oxide biosynthetic process / positive regulation of tumor necrosis factor production / defense response to virus / Potential therapeutics for SARS / 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 / apoptotic process / positive regulation of gene expression / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / membrane / plasma membrane
Similarity search - Function
Interferon gamma receptor 1, transmembrane region / Interferon gamma receptor, D2 domain, poxvirus/mammal / Interferon gamma receptor (IFNGR1), D2 domain / Interferon gamma receptor alpha subunit / Interferon gamma / Interferon gamma / : / Tissue factor / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core ...Interferon gamma receptor 1, transmembrane region / Interferon gamma receptor, D2 domain, poxvirus/mammal / Interferon gamma receptor (IFNGR1), D2 domain / Interferon gamma receptor alpha subunit / Interferon gamma / Interferon gamma / : / Tissue factor / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Interferon gamma / Interferon gamma receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.9 Å
AuthorsThiel, D.J. / le Du, M.-H. / Walter, R.L. / D'Arcy, A. / Chene, C. / Fountoulakis, M. / Garotta, G. / Winkler, F.K. / Ealick, S.E.
CitationJournal: Structure Fold.Des. / Year: 2000
Title: Observation of an unexpected third receptor molecule in the crystal structure of human interferon-gamma receptor complex.
Authors: Thiel, D.J. / le Du, M.H. / Walter, R.L. / D'Arcy, A. / Chene, C. / Fountoulakis, M. / Garotta, G. / Winkler, F.K. / Ealick, S.E.
History
DepositionJul 28, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INTERFERON GAMMA
B: INTERFERON GAMMA
C: INTERFERON-GAMMA RECEPTOR ALPHA CHAIN
D: INTERFERON-GAMMA RECEPTOR ALPHA CHAIN
E: INTERFERON-GAMMA RECEPTOR ALPHA CHAIN


Theoretical massNumber of molelcules
Total (without water)114,4105
Polymers114,4105
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)199.300, 114.650, 74.340
Angle α, β, γ (deg.)90.00, 116.27, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein INTERFERON GAMMA


Mass: 15730.941 Da / Num. of mol.: 2 / Fragment: 10 C-TERMINAL RESIDUES DELETED
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P01579
#2: Protein INTERFERON-GAMMA RECEPTOR ALPHA CHAIN


Mass: 27649.396 Da / Num. of mol.: 3 / Fragment: EXTRACELLULAR DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): SF9 INSECT CELLS / Production host: unidentified baculovirus / References: UniProt: P15260
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.33 Å3/Da / Density % sol: 63.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 12.5% PEG 8000, TRIS, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal
*PLUS
Density % sol: 61 %
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112.5 %PEG80001reservoir
2Tris-HCl1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONCHESS A110.92
SYNCHROTRONCHESS F220.9795
Detector
TypeIDDetector
PRINCETON 2K1CCD
CUSTOM-MADE2CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.921
20.97951
ReflectionResolution: 2.9→45 Å / Num. all: 33105 / Num. obs: 33105 / % possible obs: 80.1 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.056
Reflection
*PLUS
Num. measured all: 176010

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
X-PLORrefinement
RefinementResolution: 2.9→6 Å / Rfactor Rfree: 0.302 / Rfactor Rwork: 0.237
Refinement stepCycle: LAST / Resolution: 2.9→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6905 0 0 0 6905
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_angle_deg2.3
X-RAY DIFFRACTIONx_torsion_impr_deg1.9
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 6 Å / Rfactor obs: 0.237
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg2.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.93

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