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- PDB-3s8w: D2 domain of human IFNAR2 -

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Basic information

Entry
Database: PDB / ID: 3s8w
TitleD2 domain of human IFNAR2
ComponentsInterferon alpha/beta receptor 2
KeywordsSIGNALING PROTEIN RECEPTOR / human / type I interferons / receptor chain / IFNAR2 / fibronectin type III module / part of type I interferon receptor chain / interferon / extracellular space
Function / homology
Function and homology information


type I interferon receptor activity / type I interferon binding / interleukin-22 receptor activity / JAK pathway signal transduction adaptor activity / response to interferon-beta / response to interferon-alpha / type I interferon-mediated signaling pathway / cytokine binding / cell surface receptor signaling pathway via JAK-STAT / Regulation of IFNA/IFNB signaling ...type I interferon receptor activity / type I interferon binding / interleukin-22 receptor activity / JAK pathway signal transduction adaptor activity / response to interferon-beta / response to interferon-alpha / type I interferon-mediated signaling pathway / cytokine binding / cell surface receptor signaling pathway via JAK-STAT / Regulation of IFNA/IFNB signaling / cellular response to interferon-beta / response to virus / Evasion by RSV of host interferon responses / cellular response to virus / Interferon alpha/beta signaling / defense response to virus / Potential therapeutics for SARS / cell surface receptor signaling pathway / protein kinase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Interferon/interleukin receptor domain / Interferon-alpha/beta receptor, fibronectin type III / Tissue factor / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Interferon alpha/beta receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 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
DepositionMay 31, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)36,2135
Polymers36,1423
Non-polymers712
Water63135
1
A: Interferon alpha/beta receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0832
Polymers12,0471
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Interferon alpha/beta receptor 2


Theoretical massNumber of molelcules
Total (without water)12,0471
Polymers12,0471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Interferon alpha/beta receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0832
Polymers12,0471
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.660, 82.660, 225.330
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: 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: 12047.274 Da / Num. of mol.: 3 / Fragment: UNP Residues 131-232
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
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O

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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: 3.07 Å3/Da / Density % sol: 59.99 %
Crystal growTemperature: 293 K / pH: 8.5
Details: 31% (w/v) PEG 4000, 200 mM Li2SO4, 100 mM Tris pH 8.5, 5% (v/v) MPD, 10 mM Na acetate, 1.5% (w/v) PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9791
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Oct 29, 2009
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.6→19.925 Å / Num. obs: 26344 / % possible obs: 99.4 % / Redundancy: 5.6 % / Biso Wilson estimate: 45.4 Å2 / Rsym value: 9 / Net I/σ(I): 16.3
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 2.4 / Rsym value: 66.4 / % possible all: 99.2

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Processing

Software
NameClassification
Blu-Icedata collection
autoSHARPphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.6→19.925 Å / σ(F): 1.43 / Stereochemistry target values: ML
Details: ANOMALOUS SCATTERER GROUP USED FOR ATOM SE WITH FP = -3.6227 AND FDP = 5.4465
RfactorNum. reflection% reflection
Rfree0.27 1329 5.05 %
Rwork0.218 --
obs-26342 99.6 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.3 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 51.2 Å2
Baniso -1Baniso -2Baniso -3
1-8.8 Å20 Å2-0 Å2
2--8.8 Å20 Å2
3----17.59 Å2
Refinement stepCycle: LAST / Resolution: 2.6→19.925 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1950 0 2 35 1987
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0172001
X-RAY DIFFRACTIONf_angle_d1.222716
X-RAY DIFFRACTIONf_dihedral_angle_d17.257735
X-RAY DIFFRACTIONf_chiral_restr0.084324
X-RAY DIFFRACTIONf_plane_restr0.007342
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.70390.38171470.30292769X-RAY DIFFRACTION99
2.7039-2.82660.28691430.2652771X-RAY DIFFRACTION99
2.8266-2.97520.31571500.26572753X-RAY DIFFRACTION99
2.9752-3.16090.2591520.24492783X-RAY DIFFRACTION100
3.1609-3.40380.3021450.21792793X-RAY DIFFRACTION100
3.4038-3.74430.31451530.19962794X-RAY DIFFRACTION100
3.7443-4.28150.231450.19282769X-RAY DIFFRACTION100
4.2815-5.37660.20761470.16112778X-RAY DIFFRACTION100
5.3766-19.92520.26991470.24982805X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 25.2747 Å / Origin y: -26.4021 Å / Origin z: 0.5411 Å
111213212223313233
T0.117 Å2-0.0234 Å20.0032 Å2-0.1367 Å2-0.0365 Å2--0.1371 Å2
L0.7434 °20.301 °2-0.6159 °2-0.2268 °2-0.0223 °2--1.0209 °2
S-0.0554 Å °0.0162 Å °0.005 Å °0.043 Å °0.0463 Å °-0.0223 Å °-0.0029 Å °-0.0412 Å °-0.0014 Å °
Refinement TLS groupSelection details: all

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