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- PDB-2oqp: Solution structure of human interleukin-21 -

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Basic information

Entry
Database: PDB / ID: 2oqp
TitleSolution structure of human interleukin-21
ComponentsInterleukin-21
KeywordsCYTOKINE / 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 / cytokine receptor binding / tyrosine phosphorylation of STAT protein / positive regulation of natural killer cell mediated cytotoxicity / positive regulation of interleukin-17 production / positive regulation of immunoglobulin production ...T follicular helper cell differentiation / interleukin-2 receptor binding / germinal center B cell differentiation / positive regulation of tissue remodeling / Interleukin-21 signaling / cytokine receptor binding / tyrosine phosphorylation of STAT protein / positive regulation of natural killer cell mediated cytotoxicity / positive regulation of interleukin-17 production / positive regulation of immunoglobulin production / positive regulation of B cell proliferation / cell maturation / positive regulation of tyrosine phosphorylation of STAT protein / positive regulation of T cell proliferation / cytokine activity / positive regulation of cytokine production / 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
Interleukin-15/Interleukin-21 / Interleukin-15/Interleukin-21 family / Interleukin 15 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsBondensgaard, K. / Breinholt, J.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: The existence of multiple conformers of interleukin-21 directs engineering of a superpotent analogue.
Authors: Bondensgaard, K. / Breinholt, J. / Madsen, D. / Omkvist, D.H. / Kang, L. / Worsaae, A. / Becker, P. / Schiodt, C.B. / Hjorth, S.A.
History
DepositionFeb 1, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 16, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Interleukin-21


Theoretical massNumber of molelcules
Total (without water)15,6231
Polymers15,6231
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 64structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Interleukin-21 / / IL-21 / Za11


Mass: 15622.893 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL21 / Plasmid: pTAP337 / Species (production host): Escherichia coli
Production host: Escherichia coli str. K12 substr. W3110 (bacteria)
Strain (production host): W3110 / References: UniProt: Q9HBE4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1223D 13C-separated NOESY
1322D NOESY
141HNHA
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8mM IL21 U-15N, 20mM phosphate, 50mM NaCl, 1mM NaN390% H2O/10% D2O
20.8mM IL21 U-15N,13C, 20mM phosphate, 50mM NaCl, 1mM NaN3100% D2O
Sample conditionsIonic strength: 50mM NaCl / pH: 5.5 / Pressure: ambient / Temperature: 300 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 AVBrukerAV6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA1.0.8Guntert P.refinement
TALOSCornilescu G., Delaglio F., Bax A.data analysis
Sparky3.11Goddard T.D., Kneller D.G.data analysis
Felix2004Accelrysprocessing
XwinNMR3.5Brukercollection
RefinementMethod: 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 representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 64 / Conformers submitted total number: 20

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