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- PDB-1hig: THREE-DIMENSIONAL STRUCTURE OF RECOMBINANT HUMAN INTERFERON-GAMMA. -

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Basic information

Entry
Database: PDB / ID: 1hig
TitleTHREE-DIMENSIONAL STRUCTURE OF RECOMBINANT HUMAN INTERFERON-GAMMA.
ComponentsINTERFERON-GAMMAInterferon gamma
KeywordsGLYCOPROTEIN
Function / homology
Function and homology information


positive regulation of fructose 1,6-bisphosphate 1-phosphatase activity / positive regulation of iron ion import across plasma membrane / 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 / negative regulation of tau-protein kinase activity / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation involved in immune response / positive regulation of NMDA glutamate receptor activity / : / positive regulation of vitamin D biosynthetic process ...positive regulation of fructose 1,6-bisphosphate 1-phosphatase activity / positive regulation of iron ion import across plasma membrane / 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 / negative regulation of tau-protein kinase activity / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation involved in immune response / positive regulation of NMDA glutamate receptor activity / : / positive regulation of vitamin D biosynthetic process / positive regulation of interleukin-23 production / positive regulation of peptidyl-serine phosphorylation of STAT protein / negative regulation of amyloid-beta clearance / positive regulation of cellular respiration / positive regulation of smooth muscle cell apoptotic process / positive regulation of calcidiol 1-monooxygenase activity / positive regulation of protein deacetylation / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / type III interferon-mediated signaling pathway / positive regulation of core promoter binding / neuroinflammatory response / positive regulation of exosomal secretion / macrophage activation involved in immune response / positive regulation of killing of cells of another organism / negative regulation of interleukin-17 production / positive regulation of membrane protein ectodomain proteolysis / positive regulation of osteoclast differentiation / positive regulation of MHC class II biosynthetic process / positive regulation of signaling receptor activity / positive regulation of neurogenesis / negative regulation of epithelial cell differentiation / IFNG signaling activates MAPKs / positive regulation of amyloid-beta formation / positive regulation of epithelial cell migration / 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 phagocytosis / positive regulation of autophagy / type II interferon-mediated signaling pathway / Regulation of IFNG signaling / extrinsic apoptotic signaling pathway / 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 / cytokine activity / negative regulation of smooth muscle cell proliferation / astrocyte activation / positive regulation of cytokine production / positive regulation of protein-containing complex assembly / positive regulation of protein localization to plasma membrane / microglial cell activation / response to virus / positive regulation of protein serine/threonine kinase activity / cellular response to virus / positive regulation of inflammatory response / positive regulation of interleukin-6 production / positive regulation of protein import into nucleus / positive regulation of nitric oxide biosynthetic process / Interferon gamma signaling / positive regulation of tumor necrosis factor production / defense response to virus / adaptive immune response / 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 / extracellular space / extracellular region
Similarity search - Function
Interferon gamma / Interferon gamma / Four-helical cytokine-like, core
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 3.5 Å
AuthorsEalick, 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
DepositionOct 3, 1991Processing site: BNL
Revision 1.0Apr 15, 1992Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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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
D: INTERFERON-GAMMA


Theoretical massNumber of molelcules
Total (without water)64,8224
Polymers64,8224
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.000, 114.000, 315.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Atom site foot note1: RESIDUES 1, 2, 18 - 28, AND 121 - 123 FIT THE ELECTRON DENSITY POORLY.
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.081819, 0.425574, -0.901217), (0.428144, -0.801553, -0.41738), (-0.899999, -0.42, -0.116625)14.1572, 68.4508, 47.0025
2given(-0.965762, 0.219492, 0.138303), (0.218579, 0.401269, 0.889498), (0.139741, 0.889273, -0.435507)-5.8721, -6.1859, 11.0105
3given(0.036389, -0.640605, 0.767008), (-0.647516, -0.599721, -0.470167), (0.761182, -0.479541, -0.436625)1.7142, 66.1517, 53.4449
DetailsTHE 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).

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Components

#1: Protein
INTERFERON-GAMMA / Interferon gamma / Coordinate model: Cα atoms only


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

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.04 Å3/Da / Density % sol: 59.51 %
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
IDConc.Common nameCrystal-IDSol-IDDetails
1protein1drop0.0025ml
236 %satammonium sulfate1drop0.0025ml
350 mMacetate1drop
436 %satammonium sulfate1reservoir
550 mMacetate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.8 Å / Num. obs: 19954 / Num. measured all: 158195 / Rmerge(I) obs: 0.113

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 3.5→6 Å /
RfactorNum. reflection
Rwork0.25 -
obs-13192
Refinement stepCycle: LAST / Resolution: 3.5→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms492 0 0 0 492
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.022
X-RAY DIFFRACTIONx_angle_deg4.74
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
Refine-IDType
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg

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