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- PDB-3wcy: Murine Ifnar1 in complex with interferon-beta -

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Basic information

Entry
Database: PDB / ID: 3wcy
TitleMurine Ifnar1 in complex with interferon-beta
Components
  • Interferon alpha/beta receptor 1Interferon-alpha/beta receptor
  • Interferon betaInterferon type I
KeywordsCYTOKINE RECEPTOR/CYTOKINE / Fibronectin Type III / Helical cytokine / Cytokine receptor / Interferon / CYTOKINE RECEPTOR-CYTOKINE complex
Function / homology
Function and homology information


negative regulation of Lewy body formation / interferon receptor activity / type I interferon production / negative regulation of matrix metallopeptidase secretion / negative regulation of mononuclear cell migration / type I interferon receptor activity / type I interferon binding / Regulation of IFNA/IFNB signaling / type I interferon receptor binding / negative regulation of immunoglobulin production ...negative regulation of Lewy body formation / interferon receptor activity / type I interferon production / negative regulation of matrix metallopeptidase secretion / negative regulation of mononuclear cell migration / type I interferon receptor activity / type I interferon binding / Regulation of IFNA/IFNB signaling / type I interferon receptor binding / negative regulation of immunoglobulin production / Interferon alpha/beta signaling / cellular response to interferon-alpha / natural killer cell activation involved in immune response / negative regulation of blood-brain barrier permeability / positive regulation of peptidyl-serine phosphorylation of STAT protein / negative regulation of neuroinflammatory response / negative regulation of cell adhesion molecule production / positive regulation of transforming growth factor beta production / T cell activation involved in immune response / macrophage activation involved in immune response / cellular response to dsRNA / cytokine receptor activity / type I interferon-mediated signaling pathway / response to exogenous dsRNA / B cell proliferation / negative regulation of osteoclast differentiation / plasma membrane => GO:0005886 / humoral immune response / negative regulation of type II interferon production / positive regulation of autophagy / regulation of peptidyl-tyrosine phosphorylation / T cell activation / positive regulation of interferon-beta production / B cell differentiation / cellular response to dexamethasone stimulus / positive regulation of interleukin-1 beta production / cytokine activity / cellular response to virus / cytokine-mediated signaling pathway / neuron cellular homeostasis / positive regulation of type II interferon production / late endosome / defense response to virus / adaptive immune response / response to lipopolysaccharide / membrane => GO:0016020 / lysosome / defense response to bacterium / negative regulation of cell population proliferation / positive regulation of DNA-templated transcription / 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 3 domain / 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 beta / Interferon alpha/beta receptor 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsVivian, J.P. / de Weerd, N.A. / Hertzog, P.J. / Rossjohn, J.
CitationJournal: To be Published
Title: Structural basis of a unique interferon beta signaling axis mediated via the IFNAR1 receptor
Authors: de Weerd, N.A. / Vivian, J.P. / Nguyen, T.K. / Mangan, N.E. / Gould, J.A. / Braniff, S.J. / Zaker-Tabrizi, L. / Fung, K.Y. / Forster, S.C. / Beddoe, T. / Reid, H.H. / Rossjohn, J. / Hertzog, P.J.
History
DepositionJun 4, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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
I: Interferon beta


Theoretical massNumber of molelcules
Total (without water)65,5662
Polymers65,5662
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-10 kcal/mol
Surface area26480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.591, 54.591, 239.801
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Interferon alpha/beta receptor 1 / Interferon-alpha/beta receptor / IFN-R-1 / IFN-alpha/beta receptor 1 / Type I interferon receptor 1


Mass: 45805.461 Da / Num. of mol.: 1 / Fragment: extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ifar, Ifnar, Ifnar1 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: P33896
#2: Protein Interferon beta / Interferon type I / IFN-beta


Mass: 19760.926 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ifb, Ifnb, Ifnb1 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: P01575

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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: 2.72 Å3/Da / Density % sol: 54.86 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 12% PEG 3350, 8% tacsimate pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9436 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 5, 2012
RadiationMonochromator: synchrotron / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9436 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 15228 / Num. obs: 15228 / % possible obs: 98.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4 % / Biso Wilson estimate: 103.66 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 11.7
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.4 / Num. unique all: 2254 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
BUSTER2.8.0refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SE4

3se4


Resolution: 2.9→17.99 Å / Cor.coef. Fo:Fc: 0.9017 / Cor.coef. Fo:Fc free: 0.8746 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2856 777 5.1 %RANDOM
Rwork0.2368 ---
obs0.2392 15228 --
all-15228 --
Displacement parametersBiso mean: 113 Å2
Baniso -1Baniso -2Baniso -3
1--12.6509 Å20 Å20 Å2
2---12.6509 Å20 Å2
3---25.3018 Å2
Refine analyzeLuzzati coordinate error obs: 0.608 Å
Refinement stepCycle: LAST / Resolution: 2.9→17.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3896 0 0 0 3896
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1369SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes102HARMONIC2
X-RAY DIFFRACTIONt_gen_planes556HARMONIC5
X-RAY DIFFRACTIONt_it3993HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion534SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4299SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3993HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg5427HARMONIC21.04
X-RAY DIFFRACTIONt_omega_torsion2.02
X-RAY DIFFRACTIONt_other_torsion23.01
LS refinement shellResolution: 2.9→3.1 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3224 148 5.34 %
Rwork0.2497 2623 -
all0.2536 2771 -
Refinement TLS params.

T13: -0.152 Å2 / 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)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.91880.07980.557300.25282.9430.24570.0732-0.4296-0.0281-0.07830.0502-0.3377-0.5442-0.16740.02380.1141-0.11350.0843-0.12054.0415-6.9581-6.6104
25.8876-0.29942.91042.6560.21867.1060.0152-0.0377-0.319-0.00470.09870.0107-0.54420.4987-0.11380.0058-0.0582-0.11630.0421-0.303624.6352-0.71041.0579
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|9 - A|20 A|63 - A|78 A|87 - A|224 A|231 - A|282 A|290 - A|377 A|389 - A|400 }A9 - 20
2X-RAY DIFFRACTION1{ A|9 - A|20 A|63 - A|78 A|87 - A|224 A|231 - A|282 A|290 - A|377 A|389 - A|400 }A63 - 78
3X-RAY DIFFRACTION1{ A|9 - A|20 A|63 - A|78 A|87 - A|224 A|231 - A|282 A|290 - A|377 A|389 - A|400 }A87 - 224
4X-RAY DIFFRACTION1{ A|9 - A|20 A|63 - A|78 A|87 - A|224 A|231 - A|282 A|290 - A|377 A|389 - A|400 }A231 - 282
5X-RAY DIFFRACTION1{ A|9 - A|20 A|63 - A|78 A|87 - A|224 A|231 - A|282 A|290 - A|377 A|389 - A|400 }A290 - 377
6X-RAY DIFFRACTION1{ A|9 - A|20 A|63 - A|78 A|87 - A|224 A|231 - A|282 A|290 - A|377 A|389 - A|400 }A389 - 400
7X-RAY DIFFRACTION2{ I|1 - I|160 }I1 - 160

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