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- PDB-2ila: STRUCTURE OF INTERLEUKIN 1ALPHA AT 2.7-ANGSTROMS RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 2ila
TitleSTRUCTURE OF INTERLEUKIN 1ALPHA AT 2.7-ANGSTROMS RESOLUTION
ComponentsINTERLEUKIN-1 ALPHA
KeywordsCYTOKINE
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 / : / 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
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsGraves, B.J. / Hatada, M.H.
CitationJournal: Biochemistry / Year: 1990
Title: Structure of interleukin 1 alpha at 2.7-A resolution.
Authors: Graves, B.J. / Hatada, M.H. / Hendrickson, W.A. / Miller, J.K. / Madison, V.S. / Satow, Y.
History
DepositionMay 1, 1991Processing site: BNL
Revision 1.0Oct 15, 1992Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details

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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)17,6181
Polymers17,6181
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.970, 54.520, 45.630
Angle α, β, γ (deg.)90.00, 108.63, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein INTERLEUKIN-1 ALPHA / Coordinate model: Cα atoms only


Mass: 17618.033 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P01583

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.47 %
Crystal grow
*PLUS
pH: 6.2 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
135 mg/mlprotein1drop
20.1 Mcitrate1reservior
30.2 Mammonium sulphate1reservoir
430 %(w/v)PEG4001reservoir

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.19 / Highest resolution: 2.3 Å
Refinement stepCycle: LAST / Highest resolution: 2.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms145 0 0 0 145
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONx_bond_d
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scangle_it

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