- PDB-2oqp: Solution structure of human interleukin-21 -
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Basic information
Entry
Database: PDB / ID: 2oqp
Title
Solution structure of human interleukin-21
Components
Interleukin-21
Keywords
CYTOKINE / FOUR HELIX BUNDLE / MULTIPLE CONFORMERS
Function / homology
Function and homology information
T follicular helper cell differentiation / interleukin-2 receptor binding / germinal center B cell differentiation / positive regulation of tissue remodeling / Interleukin-21 signaling / positive regulation of natural killer cell mediated cytotoxicity / cytokine receptor binding / tyrosine phosphorylation of STAT protein / positive regulation of immunoglobulin production / positive regulation of interleukin-17 production ...T follicular helper cell differentiation / interleukin-2 receptor binding / germinal center B cell differentiation / positive regulation of tissue remodeling / Interleukin-21 signaling / positive regulation of natural killer cell mediated cytotoxicity / cytokine receptor binding / tyrosine phosphorylation of STAT protein / positive regulation of immunoglobulin production / positive regulation of interleukin-17 production / positive regulation of T cell proliferation / positive regulation of B cell proliferation / positive regulation of tyrosine phosphorylation of STAT protein / cell maturation / positive regulation of cytokine production / cytokine activity / cellular response to virus / positive regulation of inflammatory response / positive regulation of type II interferon production / defense response to virus / positive regulation of cell population proliferation / signal transduction / extracellular space / extracellular region Similarity search - Function
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelength
Relative weight: 1
NMR spectrometer
Type
Manufacturer
Model
Field strength (MHz)
Spectrometer-ID
Bruker AV
Bruker
AV
600
1
Varian INOVA
Varian
INOVA
800
2
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Processing
NMR software
Name
Version
Developer
Classification
CYANA
1.0.8
GuntertP.
refinement
TALOS
CornilescuG., DelaglioF., BaxA.
dataanalysis
Sparky
3.11
GoddardT.D., KnellerD.G.
dataanalysis
Felix
2004
Accelrys
processing
XwinNMR
3.5
Bruker
collection
Refinement
Method: simulated annealing / Software ordinal: 1 Details: A total of 1235, 2994 and 449 peaks from 15N-separated, 13C-separated NOESY and 2D NOESY spectra, respectively, were included in structure calculations. Together with chemical shifts for the ...Details: A total of 1235, 2994 and 449 peaks from 15N-separated, 13C-separated NOESY and 2D NOESY spectra, respectively, were included in structure calculations. Together with chemical shifts for the assigned resonances, the NOEs were analyzed with Cyana using the candid protocol for automatic NOE assignment and structure calculation. Additional sources of structural information were included in the calculations. Thus two disulfide bonds were enforced between Cys43 and Cys94, and between Cys50 and Cys97. This disulfide pattern has been established for the hIL-21 molecule through an analysis which combined protease cleavage, Edman degradation, and MS. Test calculations without disulfide bond constraints supported this pattern. Chemical shift values for HA, CA, CB, N and CO atoms were analyzed to predict phi and psi backbone angles using the computer program Talos. Talos gave good predictions for 78 residues, and 156 angle phi/psi angle constraints were included in the calculations with an uncertainty of 30 degrees. From the HNHA spectrum 72 J(HA-HN) scalar coupling constants were extracted and included in the structure calculations. Hydrogen bond constraints were added for 20 backbone amide protons which exchange slowly in deuterium exchange experiments. Hydrogen bond patterns were identified based on structures calculated without hydrogen bond constraints.
NMR representative
Selection criteria: lowest energy
NMR ensemble
Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 64 / Conformers submitted total number: 20
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