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- PDB-2l5x: Solution structure of IL1A-S100A13 complex -

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Basic information

Entry
Database: PDB / ID: 2l5x
TitleSolution structure of IL1A-S100A13 complex
Components
  • Interleukin-1 alphaInterleukin 1-alpha
  • Protein S100-A13
KeywordsCYTOKINE/TRANSPORT PROTEIN / Protein-protein complex / key component in non-classical pathway of IL-1a / Interleukin-1alpha / S100A13 / CYTOKINE-TRANSPORT PROTEIN complex
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 interleukin-1 alpha production / positive regulation of prostaglandin secretion / positive regulation of immature T cell proliferation in thymus / RAGE receptor binding ...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 interleukin-1 alpha production / positive regulation of prostaglandin secretion / positive regulation of immature T cell proliferation in thymus / RAGE receptor binding / intracellular sodium ion homeostasis / fever generation / Interleukin-1 processing / interleukin-1 receptor binding / response to copper ion / mast cell degranulation / fibroblast growth factor binding / 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 / regulation of actin cytoskeleton organization / response to gamma radiation / positive regulation of JNK cascade / cytokine-mediated signaling pathway / Interleukin-1 signaling / positive regulation of angiogenesis / positive regulation of interleukin-6 production / calcium-dependent protein binding / positive regulation of tumor necrosis factor production / protein transport / cellular response to heat / heart development / Senescence-Associated Secretory Phenotype (SASP) / spermatogenesis / Interleukin-4 and Interleukin-13 signaling / positive regulation of canonical NF-kappaB signal transduction / cellular response to lipopolysaccharide / positive regulation of ERK1 and ERK2 cascade / response to hypoxia / inflammatory response / immune response / copper ion binding / negative regulation of cell population proliferation / lipid binding / apoptotic process / calcium ion binding / positive regulation of cell population proliferation / positive regulation of gene expression / nucleolus / perinuclear region of cytoplasm / cell surface / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular space / zinc ion binding / extracellular region / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
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 / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain ...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 / S100/CaBP-9k-type, calcium binding, subdomain / S-100/ICaBP type calcium binding domain / S-100/ICaBP type calcium binding domain / Cytokine IL1/FGF / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / EF-hand / Recoverin; domain 1 / EF-hand domain pair / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Interleukin-1 alpha / Protein S100-A13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsMohan, S.K. / Yu, C.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: The IL1alpha-S100A13 heterotetrameric complex structure: a component in the non-classical pathway for interleukin 1alpha secretion
Authors: Mohan, S.K. / Yu, C.
History
DepositionNov 9, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jan 26, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 13, 2016Group: Database references
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Interleukin-1 alpha
B: Protein S100-A13
C: Protein S100-A13
D: Interleukin-1 alpha


Theoretical massNumber of molelcules
Total (without water)57,4354
Polymers57,4354
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 / 200structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

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


Mass: 17227.555 Da / Num. of mol.: 2 / Fragment: 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
#2: Protein Protein S100-A13 / S100 calcium-binding protein A13


Mass: 11490.193 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: S100A13 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q99584

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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 HN(CA)CB
1513D CBCA(CO)NH
1613D (H)CCH-TOCSY
1713D H(CCO)NH
1813D C(CO)NH
1913D HNCO
11013D 1H-15N NOESY
11113D 1H-13C NOESY
11222D 1H-15N HSQC
11322D 1H-13C HSQC
11423D HNCA
11523D HN(CA)CB
11623D CBCA(CO)NH
11723D (H)CCH-TOCSY
11823D H(CCO)NH
11923D C(CO)NH
12023D HNCO
12123D 1H-15N NOESY
12223D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.2mM [U-100% 13C; U-100% 15N] IL1A-1, 1.2mM S100A13-2, 25mM sodium phosphate-3, 100mM sodium chloride-4, 90% H2O/10% D2O90% H2O/10% D2O
21.4mM [U-100% 13C; U-100% 15N] S100A13-5, 1.4mM IL1A-6, 25 mM sodium phosphate-7, 100mM sodium chloride-8, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.2 mMIL1A-1[U-100% 13C; U-100% 15N]1
1.2 mMS100A13-21
25 mMsodium phosphate-31
100 mMsodium chloride-41
1.4 mMS100A13-5[U-100% 13C; U-100% 15N]2
1.4 mMIL1A-62
25 mMsodium phosphate-72
100 mMsodium chloride-82
Sample conditionsIonic strength: 0.1 / pH: 6.5 / Pressure: ambient atm / Temperature: 298 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
ARIA1.2 & 2.1Linge, O'Donoghue and Nilgesstructure solution
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
SparkyGoddarddata analysis
VnmrJVarianprocessing
ARIA1.2 & 2.1Linge, O'Donoghue and Nilgesrefinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: ARIA/CNS
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1

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