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- PDB-3se3: human IFNa2-IFNAR ternary complex -

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Basic information

Entry
Database: PDB / ID: 3se3
Titlehuman IFNa2-IFNAR ternary complex
Components
  • Interferon alpha 2b
  • Interferon alpha/beta receptor 1
  • Interferon alpha/beta receptor 2
KeywordsIMMUNE SYSTEM RECEPTOR / Type I interferon signaling complex / extracellular space
Function / homology
Function and homology information


type I interferon receptor activity / type I interferon binding / interleukin-22 receptor activity / type I interferon receptor binding / JAK pathway signal transduction adaptor activity / cell surface receptor signaling pathway via STAT / negative regulation of interleukin-5 production / response to interferon-beta / negative regulation of interleukin-13 production / negative regulation of T cell differentiation ...type I interferon receptor activity / type I interferon binding / interleukin-22 receptor activity / type I interferon receptor binding / JAK pathway signal transduction adaptor activity / cell surface receptor signaling pathway via STAT / negative regulation of interleukin-5 production / response to interferon-beta / negative regulation of interleukin-13 production / negative regulation of T cell differentiation / cellular response to interferon-alpha / natural killer cell activation involved in immune response / positive regulation of cellular respiration / response to interferon-alpha / positive regulation of peptidyl-serine phosphorylation of STAT protein / negative regulation of T-helper 2 cell cytokine production / T cell activation involved in immune response / negative regulation of viral entry into host cell / cytokine receptor binding / TRAF6 mediated IRF7 activation / type I interferon-mediated signaling pathway / cytokine binding / B cell proliferation / response to exogenous dsRNA / cell surface receptor signaling pathway via JAK-STAT / humoral immune response / Regulation of IFNA/IFNB signaling / cellular response to interferon-beta / B cell differentiation / cytokine activity / response to virus / Evasion by RSV of host interferon responses / cellular response to virus / cytokine-mediated signaling pathway / Interferon alpha/beta signaling / late endosome / cell-cell signaling / Factors involved in megakaryocyte development and platelet production / collagen-containing extracellular matrix / defense response to virus / adaptive immune response / Potential therapeutics for SARS / response to lipopolysaccharide / cell surface receptor signaling pathway / lysosome / inflammatory response / negative regulation of gene expression / negative regulation of DNA-templated transcription / apoptotic process / protein kinase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Interferon alpha/beta receptor 1 / Interferon alpha, beta and delta family signature. / Interferon alpha, beta and delta. / Interferon alpha/beta/delta / Interferon alpha/beta domain / Interferon/interleukin receptor domain / Interferon-alpha/beta receptor, fibronectin type III / Tissue factor / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core ...Interferon alpha/beta receptor 1 / Interferon alpha, beta and delta family signature. / Interferon alpha, beta and delta. / Interferon alpha/beta/delta / Interferon alpha/beta domain / 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 / Immunoglobulins / Immunoglobulin-like fold / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Interferon alpha-2 / Interferon alpha/beta receptor 1 / Interferon alpha/beta receptor 2 / Interferon alpha 2b
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.0001 Å
AuthorsThomas, C. / Garcia, K.C.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2011
Title: Structural linkage between ligand discrimination and receptor activation by type I interferons.
Authors: Thomas, C. / Moraga, I. / Levin, D. / Krutzik, P.O. / Podoplelova, Y. / Trejo, A. / Lee, C. / Yarden, G. / Vleck, S.E. / Glenn, J.S. / Nolan, G.P. / Piehler, J. / Schreiber, G. / Garcia, K.C.
History
DepositionJun 10, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2012Group: Database references
Revision 1.2Aug 21, 2013Group: Structure summary
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interferon alpha/beta receptor 1
B: Interferon alpha 2b
C: Interferon alpha/beta receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,1384
Polymers89,9163
Non-polymers2211
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-24 kcal/mol
Surface area30010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.370, 93.370, 401.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Interferon alpha/beta receptor 1 / IFN-R-1 / IFN-alpha/beta receptor 1 / Cytokine receptor class-II member 1 / Cytokine receptor ...IFN-R-1 / IFN-alpha/beta receptor 1 / Cytokine receptor class-II member 1 / Cytokine receptor family 2 member 1 / CRF2-1 / Type I interferon receptor 1


Mass: 47629.965 Da / Num. of mol.: 1 / Fragment: IFNa2(YNS) (UNP Residues 28-436)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IFNAR1, IFNAR / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P17181
#2: Protein Interferon alpha 2b


Mass: 19392.270 Da / Num. of mol.: 1 / Mutation: H58Y, E59N, Q62S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q86UP4, UniProt: P01563*PLUS
#3: Protein Interferon alpha/beta receptor 2 / IFN-R-2 / IFN-alpha binding protein / IFN-alpha/beta receptor 2 / Interferon alpha binding protein ...IFN-R-2 / IFN-alpha binding protein / IFN-alpha/beta receptor 2 / Interferon alpha binding protein / Type I interferon receptor 2


Mass: 22894.078 Da / Num. of mol.: 1 / Fragment: UNP Residues 34-232
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IFNAR2, IFNABR, IFNARB / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P48551
#4: 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.: 1
Source method: isolated from a genetically manipulated source
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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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.22 %
Crystal growTemperature: 293 K / pH: 6.5
Details: 15% (w/v) PEG 3350, 100 mM Na malonate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 3, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4→46.8 Å / Num. obs: 9537 / % possible obs: 99.8 % / Redundancy: 11 % / Biso Wilson estimate: 137 Å2 / Rsym value: 0.172 / Net I/σ(I): 11.7
Reflection shellResolution: 4→4.1 Å / Redundancy: 11.5 % / Mean I/σ(I) obs: 2.6 / Rsym value: 1.03 / % possible all: 100

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Processing

Software
NameClassification
Blu-Icedata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3SE4, 3S9D

3se4

3s9d


Resolution: 4.0001→46.78 Å / σ(F): 2.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.311 477 5.01 %
Rwork0.251 --
obs-9530 99.84 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 162.55 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 160.4 Å2
Baniso -1Baniso -2Baniso -3
1--6.21 Å2-0 Å20 Å2
2---6.21 Å2-0 Å2
3---12.41 Å2
Refinement stepCycle: LAST / Resolution: 4.0001→46.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4448 0 14 0 4462
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014574
X-RAY DIFFRACTIONf_angle_d1.8176242
X-RAY DIFFRACTIONf_dihedral_angle_d13.8211523
X-RAY DIFFRACTIONf_chiral_restr0.106728
X-RAY DIFFRACTIONf_plane_restr0.008794
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.0001-4.57850.32531530.23442907X-RAY DIFFRACTION100
4.5785-5.76670.31451560.21782969X-RAY DIFFRACTION100
5.7667-46.7860.30491680.2743177X-RAY DIFFRACTION100
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)
10.480.3832-0.11081.42680.11540.072-0.04870.18150.1508-0.0107-0.17180.5325-0.07060.004-0.02450.55940.1467-0.73651.171-0.25890.38110.3368-18.7501-23.1307
22.6812-0.8219-0.37340.2716-0.0520.96510.5225-0.00940.25970.0150.06950.1029-0.831-0.07540.28461.0709-0.185-0.4720.5259-0.22771.00125.7498-14.023810.6866
30.3163-0.04160.03940.4219-0.04570.0929-0.0668-0.20790.1171-0.25180.00890.23750.1396-0.0798-0.10880.35910.2099-0.52780.4341-0.45240.356135.4643-25.640218.2765
40.53620.281-0.5270.54190.04260.6758-0.58550.1680.0002-0.2465-0.1721-0.0582-0.2895-0.4208-0.02850.8369-0.0238-0.25240.65540.020.64539.2725-33.2853-12.7755
51.3585-0.1131-0.31680.6658-0.48830.47130.08990.0842-0.98340.2039-0.28690.07040.3986-0.3399-0.00251.2907-0.1277-0.0710.8594-0.15370.832134.8903-32.2404-9.4076
60.06620.06870.00010.09060.00230.0030.2166-0.4312-0.8569-0.2653-0.0172-0.43020.71560.7026-0.00251.05550.0473-0.11761.0641-0.14391.031359.7397-49.2569-13.9927
70.2462-0.5841-0.28651.27070.68260.3781-0.02720.02280.24220.0976-0.5594-0.3494-0.0843-0.325-0.00621.35110.00380.13950.9047-0.3010.99351.8943-52.2719-19.405
81.38530.24980.30010.90490.06040.21110.8576-0.3498-0.85050.6086-0.2914-1.137-0.1508-0.28770.00650.7513-0.06620.03290.8706-0.16181.021374.6321-32.666-14.536
91.1566-0.0843-1.00070.0649-0.08261.3977-0.54070.5734-0.2287-0.10880.5427-0.2612-0.3651-0.62930.01721.1326-0.25040.07260.49670.0191.173276.0711-28.8018-6.6267
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 6:104)
2X-RAY DIFFRACTION2chain 'A' and (resseq 105:232)
3X-RAY DIFFRACTION3chain 'A' and (resseq 233:302)
4X-RAY DIFFRACTION4chain 'B' and (resseq 8:66)
5X-RAY DIFFRACTION5chain 'B' and (resseq 67:156)
6X-RAY DIFFRACTION6chain 'C' and (resseq 11:29)
7X-RAY DIFFRACTION7chain 'C' and (resseq 30:104)
8X-RAY DIFFRACTION8chain 'C' and (resseq 105:139)
9X-RAY DIFFRACTION9chain 'C' and (resseq 140:204)

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