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- PDB-2lag: Structure of the 44 kDa complex of interferon-alpha2 with the ext... -

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Basic information

Entry
Database: PDB / ID: 2lag
TitleStructure of the 44 kDa complex of interferon-alpha2 with the extracellular part of IFNAR2 obtained by 2D-double difference NOESY
Components
  • Interferon alpha-2
  • Interferon alpha/beta receptor 2
KeywordsIMMUNE SYSTEM / interferon / receptor
Function / homology
Function and homology information


type I interferon receptor activity / type I interferon binding / type I interferon receptor binding / B cell activation involved in immune response / JAK pathway signal transduction adaptor activity / response to interferon-beta / natural killer cell activation involved in immune response / negative regulation of interleukin-5 production / negative regulation of interleukin-13 production / negative regulation of T cell differentiation ...type I interferon receptor activity / type I interferon binding / type I interferon receptor binding / B cell activation involved in immune response / JAK pathway signal transduction adaptor activity / response to interferon-beta / natural killer cell activation involved in immune response / negative regulation of interleukin-5 production / negative regulation of interleukin-13 production / negative regulation of T cell differentiation / response to interferon-alpha / negative regulation of T-helper 2 cell cytokine production / T cell activation involved in immune response / host-mediated suppression of symbiont invasion / cell surface receptor signaling pathway via STAT / TRAF6 mediated IRF7 activation / type I interferon-mediated signaling pathway / cytokine binding / response to exogenous dsRNA / humoral immune response / Regulation of IFNA/IFNB signaling / cell surface receptor signaling pathway via JAK-STAT / cellular response to interferon-beta / cytokine activity / Evasion by RSV of host interferon responses / cellular response to virus / response to virus / Interferon alpha/beta signaling / cell-cell signaling / : / Factors involved in megakaryocyte development and platelet production / defense response to virus / adaptive immune response / Potential therapeutics for SARS / cell surface receptor signaling pathway / receptor complex / 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 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 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 / Fibronectin type III superfamily / Immunoglobulin-like fold / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Interferon alpha-2 / Interferon alpha/beta receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model 1
AuthorsNudelman, I. / Akabayov, S.R. / Scherf, T. / Anglister, J.
CitationJournal: J.Am.Chem.Soc. / Year: 2011
Title: Observation of Intermolecular Interactions in Large Protein Complexes by 2D-Double Difference Nuclear Overhauser Enhancement Spectroscopy: Application to the 44 kDa Interferon-Receptor Complex.
Authors: Nudelman, I. / Akabayov, S.R. / Scherf, T. / Anglister, J.
History
DepositionMar 13, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 17, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2011Group: Database references
Revision 1.2Sep 28, 2011Group: Database references
Revision 1.3Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Interferon alpha/beta receptor 2
A: Interferon alpha-2


Theoretical massNumber of molelcules
Total (without water)43,5882
Polymers43,5882
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 200structures with the lowest energy
RepresentativeModel #1closest to the average

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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: 24323.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IFNAR2, IFNABR, IFNARB / Production host: Escherichia coli (E. coli) / References: UniProt: P48551
#2: Protein Interferon alpha-2 / IFN-alpha-2 / Interferon alpha-A / LeIF A


Mass: 19264.096 Da / Num. of mol.: 1 / Fragment: Extracellular domain residues 28-237
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IFNA2 / Production host: Escherichia coli (E. coli) / References: UniProt: P01563
Has protein modificationY
Sequence detailsTHE SEQUENCE FOR IFNAR2 IS FROM ISOFORM 3.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D 1H-1H NOESY

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Sample preparation

DetailsContents: 0.25 mM [U-99% 2H] Interferon alpha/beta receptor 2, 0.25 mM [U-99% 2H] Interferon alpha-2, 100% D2O
Solvent system: 100% D2O
SampleConc.: 0.25 mM / Component: protein_1-1 / Isotopic labeling: [U-99% 2H]
Sample conditionsIonic strength: 25 / pH: 8 / Pressure: ambient / Temperature: 305 K

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NMR measurement

NMR spectrometerType: Bruker Avance 3 / Manufacturer: Bruker / Model: Avance 3 / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
HADDOCKBonvinrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 10

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