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- PDB-2hym: NMR based Docking Model of the Complex between the Human Type I I... -

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Basic information

Entry
Database: PDB / ID: 2hym
TitleNMR based Docking Model of the Complex between the Human Type I Interferon Receptor and Human Interferon alpha-2
Components
  • Interferon alpha-2
  • Soluble IFN alpha/beta receptor
KeywordsIMMUNE SYSTEM / interferon receptor complex
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 / negative regulation of interleukin-5 production / response to interferon-beta / negative regulation of interleukin-13 production / negative regulation of T cell differentiation / natural killer cell activation involved in immune response ...type I interferon receptor activity / type I interferon binding / interleukin-22 receptor activity / type I interferon receptor binding / JAK pathway signal transduction adaptor activity / negative regulation of interleukin-5 production / response to interferon-beta / negative regulation of interleukin-13 production / negative regulation of T cell differentiation / natural killer cell activation involved in immune response / response to interferon-alpha / positive regulation of peptidyl-serine phosphorylation of STAT protein / cell surface receptor signaling pathway via STAT / negative regulation of T-helper 2 cell cytokine production / T cell activation involved in immune response / negative regulation of viral entry into host cell / TRAF6 mediated IRF7 activation / type I interferon-mediated signaling pathway / B cell proliferation / response to exogenous dsRNA / cytokine binding / 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 / cellular response to virus / Evasion by RSV of host interferon responses / cytokine-mediated signaling pathway / Interferon alpha/beta signaling / cell-cell signaling / Factors involved in megakaryocyte development and platelet production / defense response to virus / collagen-containing extracellular matrix / adaptive immune response / Potential therapeutics for SARS / cell surface receptor signaling pathway / 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 / 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 2 / Interferon alpha/beta receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / Rigid body docking, semi-flexible simulated annealing, refinement using explicit water
AuthorsQuadt-Akabayov, S.R. / Chill, J.H. / Levy, R. / Kessler, N. / Anglister, J.
CitationJournal: Protein Sci. / Year: 2006
Title: Determination of the human type I interferon receptor binding site on human interferon-alpha2 by cross saturation and an NMR-based model of the complex
Authors: Quadt-Akabayov, S.R. / Chill, J.H. / Levy, R. / Kessler, N. / Anglister, J.
History
DepositionAug 7, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Soluble IFN alpha/beta receptor
B: 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 / 200LOWEST ENERGY STRUCTURES OF LOWEST ENERGY CLUSTER
RepresentativeModel #6closest to the average

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Components

#1: Protein Soluble IFN alpha/beta receptor


Mass: 24323.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IFNABR / Production host: Escherichia coli (E. coli) / References: UniProt: Q15467, UniProt: P48551*PLUS
#2: Protein Interferon alpha-2 / Interferon alpha-A / LeIF A / interferon alpha 2a


Mass: 19264.096 Da / Num. of mol.: 1
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

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111TROSY HSQC with Cross Saturation
1233D 15N-separated NOESY
132HNCO
142HNCA
152HN(CA)CB
162HN(CO)CA
172HN(CA)CO
182HNCB
192HN(CO)CACB
1113TROSY HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.3 mM Interferon-alpha2 (D,15N), 90% D2O, 10% H2O, 20 mM deuterated tris buffer, 0.02% NaN390% D2O, 10% H2O
20.3 mM Interferon-alpha2 (D,15N, 13C), 5% D2O, 95% H2O, 20 mM deuterated tris buffer, 0.02% NaN35% D2O, 95% H2O
30.3 mM Interferon-alpha2 (D,15N), 5% D2O, 95% H2O, 20 mM deuterated tris buffer, 0.02% NaN35% D2O, 95% H2O
Sample conditionsIonic strength: 20 mM deuterated tris buffer / pH: 8 / Pressure: ambient / Temperature: 308 K

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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 DMXBrukerDMX5001
Bruker DRXBrukerDRX8002

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3Brukercollection
NMRPipe2.3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer, Baxprocessing
NMRView5.2.2Johnson, Blevinsdata analysis
HADDOCK1.3Dominguez, Boelens, Bonvinrefinement
RefinementMethod: Rigid body docking, semi-flexible simulated annealing, refinement using explicit water
Software ordinal: 1
Details: 1000 conformers were obtained in the rigid body docking and 200 best conformers were selected for semi-flexible simulated annealing followed by refinement
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: LOWEST ENERGY STRUCTURES OF LOWEST ENERGY CLUSTER
Conformers calculated total number: 200 / Conformers submitted total number: 10

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