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- PDB-6e3l: Interferon gamma signalling complex with IFNGR1 and IFNGR2 -

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Basic information

Entry
Database: PDB / ID: 6e3l
TitleInterferon gamma signalling complex with IFNGR1 and IFNGR2
Components
  • (Interferon gamma receptor ...) x 2
  • Interferon gamma
KeywordsCYTOKINE / cytokine receptor / protein complex / protein engineering
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 iron ion import across plasma membrane / positive regulation of cellular respiration / positive regulation of interleukin-23 production / positive regulation of smooth muscle cell apoptotic process / negative regulation of amyloid-beta clearance / type III interferon-mediated signaling pathway / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / 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 / positive regulation of osteoclast differentiation / macrophage activation involved in immune response / negative regulation of interleukin-17 production / 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 / positive regulation of amyloid-beta formation / IFNG signaling activates MAPKs / 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 / cell surface receptor signaling pathway via JAK-STAT / positive regulation of protein serine/threonine kinase activity / type II interferon-mediated signaling pathway / Regulation of IFNG signaling / positive regulation of chemokine production / extrinsic apoptotic signaling pathway / positive regulation of phagocytosis / positive regulation of interleukin-12 production / positive regulation of autophagy / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / regulation of insulin secretion / cytoplasmic vesicle membrane / 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 / astrocyte activation / negative regulation of smooth muscle cell proliferation / positive regulation of protein-containing complex assembly / microglial cell activation / cellular response to virus / positive regulation of interleukin-6 production / response to virus / positive regulation of protein import into nucleus / positive regulation of inflammatory response / cytokine-mediated signaling pathway / Interferon gamma signaling / positive regulation of nitric oxide biosynthetic process / positive regulation of tumor necrosis factor production / defense response to virus / adaptive immune response / Potential therapeutics for SARS / cell surface receptor signaling pathway / Golgi membrane / negative regulation of gene expression / negative regulation of DNA-templated transcription / apoptotic process / positive regulation of cell population proliferation / endoplasmic reticulum membrane / positive regulation of gene expression / endoplasmic reticulum / 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 / Interferon/interleukin receptor domain / Interferon-alpha/beta receptor, fibronectin type III / : / Tissue factor ...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 / Interferon/interleukin receptor domain / Interferon-alpha/beta receptor, fibronectin type III / : / Tissue factor / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Fibronectin type-III domain profile. / 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
CYSTEINE / Interferon gamma / Interferon gamma receptor 1 / Interferon gamma receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsJude, K.M. / Mendoza, J.L. / Garcia, K.C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)RO1-AI51321 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)K01CA175127 United States
CitationJournal: Nature / Year: 2019
Title: Structure of the IFN gamma receptor complex guides design of biased agonists.
Authors: Mendoza, J.L. / Escalante, N.K. / Jude, K.M. / Sotolongo Bellon, J. / Su, L. / Horton, T.M. / Tsutsumi, N. / Berardinelli, S.J. / Haltiwanger, R.S. / Piehler, J. / Engleman, E.G. / Garcia, K.C.
History
DepositionJul 14, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 20, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Oct 23, 2024Group: Structure summary / Category: 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 1
D: Interferon gamma receptor 1
E: Interferon gamma receptor 2
I: Interferon gamma receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,23620
Polymers141,7826
Non-polymers5,45414
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.694, 150.212, 212.668
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Interferon gamma receptor ... , 2 types, 4 molecules CDEI

#2: Protein Interferon gamma receptor 1 / IFN-gamma-R1 / CDw119 / Interferon gamma receptor alpha-chain / IFN-gamma-R-alpha


Mass: 27363.729 Da / Num. of mol.: 2 / Mutation: T149I, M161K, Q167K, K174N, Q182R, H205N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IFNGR1 / Cell line (production host): HEK 293 / Production host: Homo sapiens (human) / References: UniProt: P15260
#3: Protein Interferon gamma receptor 2 / IFN-gamma-R2 / Interferon gamma receptor accessory factor 1 / AF-1 / Interferon gamma receptor beta- ...IFN-gamma-R2 / Interferon gamma receptor accessory factor 1 / AF-1 / Interferon gamma receptor beta-chain / IFN-gamma-R-beta / Interferon gamma transducer 1


Mass: 26310.582 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IFNGR2, IFNGT1 / Cell line (production host): HEK 293 / Production host: Homo sapiens (human) / References: UniProt: P38484

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Protein / Non-polymers , 2 types, 4 molecules AB

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


Mass: 17216.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IFNG / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P01579
#8: Chemical ChemComp-CYS / CYSTEINE


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C3H7NO2S

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Sugars , 4 types, 12 molecules

#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 3 / Source method: obtained synthetically
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#6: Polysaccharide alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e6-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#7: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Details

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: 4.47 Å3/Da / Density % sol: 72.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.1 M Ammonium Tartrate dibasic pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.999989 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999989 Å / Relative weight: 1
ReflectionResolution: 3.8→48.74 Å / Num. obs: 25652 / % possible obs: 99.9 % / Redundancy: 14.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.271 / Rpim(I) all: 0.073 / Rrim(I) all: 0.281 / Χ2: 0.99 / Net I/σ(I): 10
Reflection shellResolution: 3.8→3.9 Å / Redundancy: 14.9 % / Rmerge(I) obs: 3.524 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 1875 / CC1/2: 0.429 / Rpim(I) all: 0.942 / Rrim(I) all: 3.649 / Χ2: 0.96 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.14_3211refinement
XDSJan 26, 2018data reduction
Aimless0.7.1data scaling
PHASER2.8.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6E3K

6e3k


Resolution: 3.8→48.738 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.65
RfactorNum. reflection% reflection
Rfree0.2724 1689 6.61 %
Rwork0.2477 --
obs0.2493 25570 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.8→48.738 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8619 0 357 0 8976
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049223
X-RAY DIFFRACTIONf_angle_d0.80112583
X-RAY DIFFRACTIONf_dihedral_angle_d11.1525508
X-RAY DIFFRACTIONf_chiral_restr0.0631456
X-RAY DIFFRACTIONf_plane_restr0.0041577
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.8001-3.91190.45141400.40481966X-RAY DIFFRACTION100
3.9119-4.03810.34441360.35281947X-RAY DIFFRACTION100
4.0381-4.18240.32811400.31011971X-RAY DIFFRACTION100
4.1824-4.34970.33171390.29111971X-RAY DIFFRACTION100
4.3497-4.54750.25071370.23791949X-RAY DIFFRACTION100
4.5475-4.78710.24581380.22111936X-RAY DIFFRACTION100
4.7871-5.08670.25651410.22951999X-RAY DIFFRACTION100
5.0867-5.4790.23671400.22361975X-RAY DIFFRACTION100
5.479-6.02950.2721390.24482005X-RAY DIFFRACTION100
6.0295-6.89980.24831420.25961999X-RAY DIFFRACTION100
6.8998-8.6850.28571460.23792048X-RAY DIFFRACTION100
8.685-48.7420.25071510.22092115X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9429-1.7385-0.63870.32231.1671.9968-0.09130.02490.03670.0403-0.1274-0.20.21110.660801.27710.2868-0.05631.03820.00581.232-18.41274.83261.3691
20.94840.99491.1552.4114-0.55981.17740.30030.39170.2108-0.0728-0.3231-0.02480.5745-0.092501.17410.31610.10150.618-00.8718-16.1619-4.582813.0066
31.572-0.5474-0.13440.31070.57870.1621-0.08550.1010.19410.0678-0.16010.27580.8944-0.0162-0.3271.14670.06260.14191.2673-0.15251.2018-31.9185-1.4035-27.4179
4-1.07480.83010.16140.17941.57660.76370.1558-0.24570.25690.4082-0.263-0.09150.4546-0.2743-1.09171.6095-0.0781-0.21581.37340.15981.1417-31.3316-4.462541.3941
5-0.6433-0.814-0.26321.6704-0.8827-0.26730.60290.1213-0.71730.79890.42280.81680.66310.60330.00013.9383-0.0049-0.37133.72310.54373.1956-26.3417-33.39521.8224
63.1494-0.2080.7822-0.31960.95911.3314-0.3225-0.03280.329-0.0871-0.07670.28310.0284-0.170200.6937-0.01170.00650.90670.02331.1925-41.072326.2064-7.9006
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID -1:123 )A-1 - 123
2X-RAY DIFFRACTION2( CHAIN B AND RESID -1:124 )B-1 - 124
3X-RAY DIFFRACTION3( CHAIN C AND RESID 11:223 )C11 - 223
4X-RAY DIFFRACTION4( CHAIN D AND RESID 11:221 )D11 - 221
5X-RAY DIFFRACTION5( CHAIN E AND RESID 28:240 )E28 - 240
6X-RAY DIFFRACTION6( CHAIN I AND RESID 28:240 )I28 - 240

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