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- PDB-1n6u: NMR structure of the interferon-binding ectodomain of the human i... -

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Basic information

Entry
Database: PDB / ID: 1n6u
TitleNMR structure of the interferon-binding ectodomain of the human interferon receptor
ComponentsInterferon-alpha/beta receptor beta chain
KeywordsIMMUNE SYSTEM / immunoglobulin fold / fibronectin fold / two-domain structure
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 / Evasion by RSV of host interferon responses / response to virus / 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)
MethodSOLUTION NMR / distance geometry, simulated annealing
AuthorsChill, J.H. / Quadt, S.R. / Levy, R. / Schreiber, G. / Anglister, J.
Citation
Journal: Structure / Year: 2003
Title: The human type I interferon receptor. NMR structure reveals the molecular basis of ligand binding.
Authors: Chill, J.H. / Quadt, S.R. / Levy, R. / Schreiber, G. / Anglister, J.
#1: Journal: Biochemistry / Year: 2002
Title: The human interferon receptor: NMR-based modeling, mapping of the IFN-alpha2 binding site, and observed ligand-induced tightening
Authors: Chill, J.H. / Nivasch, R. / Levy, R. / Albeck, S. / Schreiber, G. / Anglister, J.
History
DepositionNov 12, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Interferon-alpha/beta receptor beta chain


Theoretical massNumber of molelcules
Total (without water)24,3231
Polymers24,3231
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)22 / 35structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Interferon-alpha/beta receptor beta chain / IFN-alpha-REC / Type I interferon receptor / IFN-R / Interferon alpha/beta receptor- 2


Mass: 24323.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IFNAR2 OR IFNARB / Production host: Escherichia coli (E. coli) / Strain (production host): TG1 / References: UniProt: P48551

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
121HNHA
232HNCA
242HN(CA)CB
252CBCA(CO)NH
3633D 13C-separated NOESY
NMR detailsText: Experiments all performed in Shigemi tubed equipped with inserts

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5mM IFNAR2-EC U-15N; 20mM d-Tris pH 8, 0.02% NaN3;95% H2O/5% D2O
20.35mM IFNAR2-EC U-15N,13C; 20mM d-Tris pH 8, 0.02% NaN3;95% H2O/5% D2O
30.35mM IFNAR2-EC U-15N,13C; 20mM d-Tris pH 8, 0.02% NaN3;99% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
120mM Tris 8 ambient 308 K
220mM Tris 8 ambient 308 K
320mM Tris 8 ambient 305 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX8001
Bruker DMXBrukerDMX5002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3Neidigprocessing
CNS1.1Brungerstructure solution
NMRPipe2.1Delagliodata analysis
CNS1.1Brungerrefinement
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1
Details: the structures are based on a total of 1947 inter-residual NOE-derived distance restraints (of which 1066 are long range), 172 dihedral angle restraints (88 experimental and 84 TALOS-derived) ...Details: the structures are based on a total of 1947 inter-residual NOE-derived distance restraints (of which 1066 are long range), 172 dihedral angle restraints (88 experimental and 84 TALOS-derived), 138 distance restraints from hydrogen bonds, and 109 residual dipolar coupling restraints.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 35 / Conformers submitted total number: 22

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