- 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
Title
NMR 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
Keywords
IMMUNE 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 / 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
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
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Experimental details
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Experiment
Experiment
Method: SOLUTION NMR
NMR experiment
Conditions-ID
Experiment-ID
Solution-ID
Type
1
1
1
TROSYHSQC with Cross Saturation
1
2
3
3D 15N-separated NOESY
1
3
2
HNCO
1
4
2
HNCA
1
5
2
HN(CA)CB
1
6
2
HN(CO)CA
1
7
2
HN(CA)CO
1
8
2
HNCB
1
9
2
HN(CO)CACB
1
11
3
TROSYHSQC
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Sample preparation
Details
Solution-ID
Contents
Solvent system
1
0.3 mM Interferon-alpha2 (D,15N), 90% D2O, 10% H2O, 20 mM deuterated tris buffer, 0.02% NaN3
90% D2O, 10% H2O
2
0.3 mM Interferon-alpha2 (D,15N, 13C), 5% D2O, 95% H2O, 20 mM deuterated tris buffer, 0.02% NaN3
5% D2O, 95% H2O
3
0.3 mM Interferon-alpha2 (D,15N), 5% D2O, 95% H2O, 20 mM deuterated tris buffer, 0.02% NaN3
5% D2O, 95% H2O
Sample conditions
Ionic strength: 20 mM deuterated tris buffer / pH: 8 / Pressure: ambient / Temperature: 308 K
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NMR measurement
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelength
Relative weight: 1
NMR spectrometer
Type
Manufacturer
Model
Field strength (MHz)
Spectrometer-ID
Bruker DMX
Bruker
DMX
500
1
Bruker DRX
Bruker
DRX
800
2
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Processing
NMR software
Name
Version
Developer
Classification
XwinNMR
3
Bruker
collection
NMRPipe
2.3
Delaglio, Grzesiek, Vuister, Zhu, Pfeifer, Bax
processing
NMRView
5.2.2
Johnson, Blevins
dataanalysis
HADDOCK
1.3
Dominguez, Boelens, Bonvin
refinement
Refinement
Method: 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 representative
Selection criteria: closest to the average
NMR ensemble
Conformer selection criteria: LOWEST ENERGY STRUCTURES OF LOWEST ENERGY CLUSTER Conformers calculated total number: 200 / Conformers submitted total number: 10
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