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- PDB-1fyh: 1:1 COMPLEX BETWEEN AN INTERFERON GAMMA SINGLE-CHAIN VARIANT AND ... -

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Basic information

Entry
Database: PDB / ID: 1fyh
Title1:1 COMPLEX BETWEEN AN INTERFERON GAMMA SINGLE-CHAIN VARIANT AND ITS RECEPTOR
Components
  • Interferon gamma
  • Interferon gamma receptor 1
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: 2.04 Å
AuthorsRandal, 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
DepositionSep 29, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 21, 2017Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity.pdbx_fragment ..._entity.pdbx_description / _entity.pdbx_fragment / _struct_ref_seq.db_align_end / _struct_ref_seq.ref_id / _struct_ref_seq_dif.details
Revision 1.4Nov 6, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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 receptor 1
D: Interferon gamma
E: Interferon gamma receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,1285
Polymers112,0934
Non-polymers351
Water8,665481
1
A: Interferon gamma
B: Interferon gamma receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0823
Polymers56,0462
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Interferon gamma
E: Interferon gamma receptor 1


Theoretical massNumber of molelcules
Total (without water)56,0462
Polymers56,0462
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.940, 107.600, 85.080
Angle α, β, γ (deg.)90.00, 97.94, 90.00
Int Tables number4
Space group name H-MP1211
Detailsthe biological assembly consists of one single-chain interferon gamma and one receptor

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Components

#1: Protein Interferon gamma / IFN-gamma / Immune interferon


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 Interferon gamma receptor 1 / IFN-gamma-R1 / CDw119 / Interferon gamma receptor alpha-chain / IFN-gamma-R-alpha


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 / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 481 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.95 Å3/Da / Density % sol: 58.29 %
Crystal growTemperature: 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
IDConc.Common nameCrystal-IDSol-ID
12 Mammonium sulfate1reservoir
28 %PEG80001reservoir
3100 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.91
DetectorType: ADSC / Detector: CCD / Date: May 16, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.851refinement
X-PLORphasing
RefinementResolution: 2.04→15 Å / Rfactor Rfree error: 0.003 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.246 7119 9.1 %RANDOM
Rwork0.194 ---
all0.241 78548 --
obs0.241 78548 95.2 %-
Displacement parametersBiso mean: 35.8 Å2
Baniso -1Baniso -2Baniso -3
1-4.4813 Å20 Å22.0958 Å2
2---11.0017 Å20 Å2
3---6.5204 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a25 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.04→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7205 0 1 481 7687
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1.85
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_dihedral_angle_d25.1
X-RAY DIFFRACTIONx_improper_angle_d1.08
X-RAY DIFFRACTIONx_mcbond_it2.9553
X-RAY DIFFRACTIONx_mcangle_it3.9864.3
X-RAY DIFFRACTIONx_scbond_it9.6964.8
X-RAY DIFFRACTIONx_scangle_it11.2855.8
LS refinement shellResolution: 2.04→2.11 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.299 591 8.9 %
Rwork0.256 6083 -
obs--81.1 %
Xplor fileSerial no: 1 / Param file: parhcsdx.pro / Topol file: tophcsdx.pro
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.08

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