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- PDB-1ga3: NMR STRUCTURE OF INTERLEUKIN-13 -

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Basic information

Entry
Database: PDB / ID: 1ga3
TitleNMR STRUCTURE OF INTERLEUKIN-13
ComponentsInterleukin-13
KeywordsCYTOKINE
Function / homology
Function and homology information


interleukin-13 receptor binding / negative regulation of lung ciliated cell differentiation / positive regulation of lung goblet cell differentiation / positive regulation of pancreatic stellate cell proliferation / interleukin-13-mediated signaling pathway / regulation of proton transport / negative regulation of complement-dependent cytotoxicity / Interleukin-18 signaling / negative regulation of transforming growth factor beta production / positive regulation of mast cell degranulation ...interleukin-13 receptor binding / negative regulation of lung ciliated cell differentiation / positive regulation of lung goblet cell differentiation / positive regulation of pancreatic stellate cell proliferation / interleukin-13-mediated signaling pathway / regulation of proton transport / negative regulation of complement-dependent cytotoxicity / Interleukin-18 signaling / negative regulation of transforming growth factor beta production / positive regulation of mast cell degranulation / macrophage activation / response to selenium ion / response to nematode / positive regulation of macrophage activation / positive regulation of immunoglobulin production / positive regulation of interleukin-10 production / negative regulation of endothelial cell apoptotic process / positive regulation of B cell proliferation / positive regulation of smooth muscle cell proliferation / positive regulation of release of sequestered calcium ion into cytosol / cytokine activity / positive regulation of protein secretion / response to nicotine / microglial cell activation / cellular response to mechanical stimulus / negative regulation of inflammatory response / positive regulation of cold-induced thermogenesis / response to ethanol / Interleukin-4 and Interleukin-13 signaling / response to lipopolysaccharide / immune response / inflammatory response / external side of plasma membrane / positive regulation of gene expression / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / cytoplasm
Similarity search - Function
Interleukin-13 / Interleukin-13 / Interleukin-4/interleukin-13 / Interleukin-4/interleukin-13, conserved site / Interleukins -4 and -13 signature. / Interleukins 4 and 13 / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsEisenmesser, E.Z. / Horita, D.A. / Altieri, A.S. / Byrd, R.A.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: Solution structure of interleukin-13 and insights into receptor engagement
Authors: Eisenmesser, E.Z. / Horita, D.A. / Altieri, A.S. / Byrd, R.A.
#1: Journal: J.BIOMOL.NMR / Year: 2001
Title: Secondary Structure and Backbone Resonance Assignments for Human Interleukin-13
Authors: Eisenmesser, E.Z. / Horita, D.A. / Byrd, R.A.
#2: Journal: Protein Expr.Purif. / Year: 2000
Title: Expression, Purification, Refolding, and Characterization of Recombinant Human Interleukin-13: Utilization of Intracellular Processing
Authors: Eisenmesser, E.Z. / Kapust, R.B. / Nawrocki, J.P. / Waugh, D.S. / Byrd, R.A. / Mazzulla, M.J. / Pannell, L.K.
History
DepositionNov 29, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 25, 2019Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_related ...database_2 / pdbx_database_related / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _struct_ref_seq_dif.details
Revision 2.0Feb 26, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Experimental preparation / Other / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_name_com / entity_src_gen / pdbx_database_status / pdbx_nmr_exptl / pdbx_nmr_exptl_sample / pdbx_nmr_exptl_sample_conditions / pdbx_nmr_refine / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_struct_sheet_hbond / pdbx_validate_torsion / pdbx_version / struct / struct_conf / struct_keywords / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _entity.pdbx_description / _entity.pdbx_fragment / _entity_name_com.name / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_seq_type / _pdbx_database_status.SG_entry / _pdbx_nmr_exptl.sample_state / _pdbx_nmr_exptl.spectrometer_id / _pdbx_nmr_exptl_sample_conditions.ionic_strength_units / _pdbx_nmr_exptl_sample_conditions.label / _pdbx_nmr_exptl_sample_conditions.pH_units / _pdbx_nmr_refine.software_ordinal / _pdbx_nmr_sample_details.contents / _pdbx_nmr_sample_details.label / _pdbx_nmr_sample_details.type / _pdbx_nmr_software.authors / _pdbx_nmr_software.classification / _pdbx_nmr_software.version / _pdbx_struct_sheet_hbond.range_1_auth_atom_id / _pdbx_struct_sheet_hbond.range_1_label_atom_id / _pdbx_struct_sheet_hbond.range_2_auth_atom_id / _pdbx_struct_sheet_hbond.range_2_label_atom_id / _pdbx_struct_sheet_hbond.sheet_id / _struct.pdbx_CASP_flag / _struct_conf.pdbx_PDB_helix_id / _struct_keywords.text / _struct_ref.pdbx_align_begin / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details / _struct_sheet.id / _struct_sheet_order.sheet_id / _struct_sheet_range.sheet_id
Description: Model orientation/position / Provider: author / Type: Coordinate replacement
Revision 2.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 2.2Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Interleukin-13


Theoretical massNumber of molelcules
Total (without water)12,4161
Polymers12,4161
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Interleukin-13 / IL-13 / IL13


Mass: 12416.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL13, NC30 / Plasmid: PMAL-IL-13 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P35225
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D 15N-separated NOESY
121isotropic13D 13C-separated NOESY
131isotropic1HN(CA)CB
141isotropic1CACBCONH
151isotropic24D CC-NOESY
161isotropic24D CN-NOESY
NMR detailsText: Using 3D and 4D NMR.

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Sample preparation

DetailsType: solution
Contents: 1 mM [U-100% 13C; U-100% 15N] IL-13, 25 mM phosphate buffer, 50 mM sodium chloride, 1 mM EDTA, 95% H2O/5% D2O
Label: sample1 / Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMIL-13[U-100% 13C; U-100% 15N]1
25 mMphosphate buffernatural abundance1
50 mMsodium chloridenatural abundance1
1 mMEDTAnatural abundance1
Sample conditionsIonic strength: 50mM NaCl Not defined / Label: cond1 / pH: 6.1 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
ANSIGKraulisdata analysis
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
ARIALinge, O'Donoghue and Nilgesstructure calculation
ARIALinge, O'Donoghue and Nilgesrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 5
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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