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- PDB-2kki: Solution structure of human Interleukin 1a -

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Basic information

Entry
Database: PDB / ID: 2kki
TitleSolution structure of human Interleukin 1a
ComponentsInterleukin-1 alpha
KeywordsCYTOKINE / Protein / Glycoprotein / Inflammatory response / Lipoprotein / Mitogen / Myristate / Polymorphism / Pyrogen / Secreted
Function / homology
Function and homology information


negative regulation of establishment of Sertoli cell barrier / positive regulation of neutrophil migration / positive regulation of steroid biosynthetic process / connective tissue replacement involved in inflammatory response wound healing / response to L-ascorbic acid / response to ozone / positive regulation of prostaglandin secretion / positive regulation of stress-activated MAPK cascade / positive regulation of immature T cell proliferation in thymus / fever generation ...negative regulation of establishment of Sertoli cell barrier / positive regulation of neutrophil migration / positive regulation of steroid biosynthetic process / connective tissue replacement involved in inflammatory response wound healing / response to L-ascorbic acid / response to ozone / positive regulation of prostaglandin secretion / positive regulation of stress-activated MAPK cascade / positive regulation of immature T cell proliferation in thymus / fever generation / intracellular sodium ion homeostasis / Interleukin-1 processing / interleukin-1 receptor binding / response to copper ion / keratinization / Interleukin-10 signaling / positive regulation of cell division / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of vascular endothelial growth factor production / ectopic germ cell programmed cell death / Pyroptosis / Purinergic signaling in leishmaniasis infection / extrinsic apoptotic signaling pathway in absence of ligand / response to organonitrogen compound / positive regulation of interleukin-2 production / positive regulation of mitotic nuclear division / positive regulation of cytokine production / cytokine activity / positive regulation of protein secretion / response to gamma radiation / regulation of actin cytoskeleton organization / positive regulation of JNK cascade / cytokine-mediated signaling pathway / Interleukin-1 signaling / positive regulation of angiogenesis / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / heart development / cellular response to heat / Senescence-Associated Secretory Phenotype (SASP) / spermatogenesis / cellular response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / positive regulation of canonical NF-kappaB signal transduction / positive regulation of ERK1 and ERK2 cascade / response to hypoxia / inflammatory response / immune response / copper ion binding / negative regulation of cell population proliferation / apoptotic process / positive regulation of gene expression / cell surface / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / nucleus / cytosol
Similarity search - Function
Interleukin-1 alpha / Interleukin-1 propeptide / Interleukin-1 propeptide / Interleukin-1 conserved site / Interleukin-1 signature. / Interleukin-1 homologues / Interleukin-1 family / Interleukin-1 / 18 / Cytokine IL1/FGF / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 ...Interleukin-1 alpha / Interleukin-1 propeptide / Interleukin-1 propeptide / Interleukin-1 conserved site / Interleukin-1 signature. / Interleukin-1 homologues / Interleukin-1 family / Interleukin-1 / 18 / Cytokine IL1/FGF / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsMohan, S.K. / Chang, H.-K. / Yu, C.
CitationJournal: Biomol.Nmr Assign. / Year: 2010
Title: 1H, 13C and 15N backbone and side chain resonance assignments of human interleukin 1alpha
Authors: Chang, H.-K. / Mohan, S.K. / Chin, Y.
History
DepositionJun 24, 2009Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jun 30, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Interleukin-1 alpha


Theoretical massNumber of molelcules
Total (without water)17,2281
Polymers17,2281
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)14 / 200structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Interleukin-1 alpha / IL-1 alpha / Hematopoietin-1


Mass: 17227.555 Da / Num. of mol.: 1 / Fragment: UNP residues 121-271
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL1A, IL1F1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: P01583

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCA
1413D HNCO
1513D HN(CO)CA
1613D CBCA(CO)NH
1713D HBHA(CO)NH
1813D H(CCO)NH
1913D (H)CCH-TOCSY
11013D C(CO)NH
11113D 1H-15N NOESY
11213D 1H-13C NOESY

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Sample preparation

DetailsContents: 10mM TRIS, 100mM sodium chloride, 1.4mM protein, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
10 mMTRIS-11
100 mMsodium chloride-21
1.4 mMentity-31
Sample conditionsIonic strength: 0.1 / pH: 7.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian VNMRS / Manufacturer: Varian / Model: VNMRS / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
ARIA1.1Dr. Michael Nilges, Institut Pasteurautomated noe assignment
ARIA1.1Dr. Michael Nilges, Institut Pasteurnmr structure calculation
SparkyGoddardchemical shift assignment
TALOSCornilescu, Delaglio and Baxdihedral angles
VnmrJVNMRJ_2.2CVarianprocessing
CNSrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 14 / Representative conformer: 1

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