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- PDB-2kz1: Inter-molecular interactions in a 44 kDa interferon-receptor comp... -

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Basic information

Entry
Database: PDB / ID: 2kz1
TitleInter-molecular interactions in a 44 kDa interferon-receptor complex detected by asymmetric back-protonation and 2D NOESY
Components
  • Interferon alpha-2
  • Soluble IFN alpha/beta receptor
KeywordsANTIVIRAL PROTEIN / INTERFERON / RECEPTOR / DOCKING / COMPLEX / ANTIVIRAL DEFENSE / CYTOKINE / DISULFIDE BOND / GLYCOPROTEIN / SECRETED
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 / cell surface receptor signaling pathway via STAT / negative regulation of interleukin-5 production / response to interferon-beta / negative regulation of interleukin-13 production / negative regulation of T cell differentiation ...type I interferon receptor activity / type I interferon binding / interleukin-22 receptor activity / type I interferon receptor binding / JAK pathway signal transduction adaptor activity / cell surface receptor signaling pathway via STAT / 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 / 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 / cytokine binding / response to exogenous dsRNA / B cell proliferation / 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 / Evasion by RSV of host interferon responses / cellular response to virus / cytokine-mediated signaling pathway / Interferon alpha/beta signaling / cell-cell signaling / Factors involved in megakaryocyte development and platelet production / collagen-containing extracellular matrix / defense response to virus / 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 / Growth Hormone; Chain: A; ...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 / simulated annealing, molecular dynamics
Model detailsclosest to the average, model 4
AuthorsNudelman, I. / Akabayov, S.R. / Schnur, E. / Biron, Z. / Levy, R. / Xu, Y. / Yang, D. / Anglister, J.
CitationJournal: Biochemistry / Year: 2010
Title: Intermolecular interactions in a 44 kDa interferon-receptor complex detected by asymmetric reverse-protonation and two-dimensional NOESY
Authors: Nudelman, I. / Akabayov, S.R. / Schnur, E. / Biron, Z. / Levy, R. / Xu, Y. / Yang, D. / Anglister, J.
History
DepositionJun 10, 2010Deposition site: BMRB / Processing site: RCSB
SupersessionJun 23, 2010ID: 2KSX
Revision 1.0Jun 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 18, 2021Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Refinement description
Category: database_2 / pdbx_nmr_exptl ...database_2 / pdbx_nmr_exptl / pdbx_nmr_exptl_sample / pdbx_nmr_exptl_sample_conditions / pdbx_nmr_refine / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_exptl.conditions_id / _pdbx_nmr_exptl.solution_id / _pdbx_nmr_exptl_sample_conditions.pressure_units / _pdbx_nmr_exptl_sample_conditions.temperature / _pdbx_nmr_refine.software_ordinal / _pdbx_nmr_sample_details.contents / _pdbx_nmr_sample_details.label / _pdbx_nmr_sample_details.solvent_system / _pdbx_nmr_sample_details.type / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


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_5551
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-2 / IFN-alpha-2 / Interferon alpha-A / LeIF A


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) / Strain (production host): ROSETTA / References: UniProt: P01563
#2: 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) / Strain (production host): ROSETTA / References: UniProt: Q15467, UniProt: P48551*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: docking model of IFNAR2-EC/IFNalpha2 complex
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1222D 1H-1H NOESY
1332D 1H-1H NOESY
1443D 15N NOESY
1553D 15N NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.25 mM [U-99% 2H] Interferon alpha, 0.25 mM [U-99% 2H] Soluble IFN alpha/beta receptor, 25 mM [U-2H] TRIS, 0.02 % sodium azide, 100% D2Osample_1100% D2O
solution20.25 MM [U-99% 2H, 1H-K,R,L,A,M] INTERFERON ALPHA2, 0.25 MM [U-99% 2H, 1H-H,F,W] SOLUBLE IFN ALPHA/BETA RECEPTOR, 25 mM [U-2H] TRIS, 0.02 % sodium azide, 100% D2Osample_2100% D2O
solution30.25 MM [U-99% 2H, 1H-L] INTERFERON ALPHA2, 0.25 MM [U-99% 2H, 1H-H,W] SOLUBLE IFN ALPHA/BETA RECEPTOR, 25 mM [U-2H] TRIS, 0.02 % sodium azide, 100% D2Osample_3100% D2O
solution40.25 MM [15N] INTERFERON ALPHA2, 0.25 MM [1H] SOLUBLE IFN ALPHA/BETA RECEPTOR, 25 mM [U-2H] TRIS, 0.02 % sodium azide, 95% H2O/5% D2Osample_495% H2O/5% D2O
solution50.25 MM [1H] INTERFERON ALPHA2, 0.25 MM [15N] SOLUBLE IFN ALPHA/BETA RECEPTOR, 25 mM [U-2H] TRIS, 0.02 % sodium azide, 95% H2O/5% D2Osample_595% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.25 mMINTERFERON ALPHA-2[U-2H]1
0.25 mMSOLUBLE IFN ALPHA/BETA RECEPTOR[U-2H]1
25 mMTRIS[U-2H]1
0.02 %sodium azidenatural abundance1
0.25 mMINTERFERON ALPHA-2[U-99% 2H, 1H-K,R,L,A,M]2
0.25 mMSOLUBLE IFN ALPHA/BETA RECEPTOR[U-99% 2H, 1H-H,F,W]2
25 mMTRIS[U-2H]2
0.02 %sodium azidenatural abundance2
0.25 mMINTERFERON ALPHA-2[U-99% 2H, 1H-L]3
0.25 mMSOLUBLE IFN ALPHA/BETA RECEPTOR[U-99% 2H, 1H-H,W]3
25 mMTRIS[U-2H]3
0.02 %sodium azidenatural abundance3
0.25 mMINTERFERON ALPHA-2[15N]4
0.25 mMSOLUBLE IFN ALPHA/BETA RECEPTOR[1H]4
25 mMTRIS[U-2H]4
0.02 %sodium azidenatural abundance4
0.25 mMINTERFERON ALPHA-2[1H]5
0.25 mMSOLUBLE IFN ALPHA/BETA RECEPTOR[15N]5
25 mMTRIS[U-2H]5
0.02 %sodium azidenatural abundance5
Sample conditionsIonic strength: 25 / pH: 8.0 / Pressure: ambient / Temperature: 305 K

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NMR measurement

NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
HADDOCK2Dominguez et al.refinement
XwinNMR3Bruker Biospincollection
NMRView5.2.2Johnson, One Moon Scientificdata analysis
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 2
Details: 1000 CONFORMERS WERE OBTAINED IN THE RIGID BODY DOCKING AND 200 BEST CONFORMERS WERE SELECTED FOR SEMI-FLEXIBLE SIMULATED ANNEALING FOLLOWED BY REFINEMENT IN WATER
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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