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- PDB-1i1b: CRYSTAL STRUCTURE OF RECOMBINANT HUMAN INTERLEUKIN-1BETA AT 2.0 A... -

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Basic information

Entry
Database: PDB / ID: 1i1b
TitleCRYSTAL STRUCTURE OF RECOMBINANT HUMAN INTERLEUKIN-1BETA AT 2.0 ANGSTROMS RESOLUTION
ComponentsINTERLEUKIN-1 BETA
KeywordsCYTOKINE
Function / homology
Function and homology information


positive regulation of T cell mediated immunity / positive regulation of cell adhesion molecule production / negative regulation of adiponectin secretion / monocyte aggregation / negative regulation of lipid metabolic process / smooth muscle adaptation / positive regulation of lipid catabolic process / negative regulation of D-glucose transmembrane transport / regulation of nitric-oxide synthase activity / hyaluronan biosynthetic process ...positive regulation of T cell mediated immunity / positive regulation of cell adhesion molecule production / negative regulation of adiponectin secretion / monocyte aggregation / negative regulation of lipid metabolic process / smooth muscle adaptation / positive regulation of lipid catabolic process / negative regulation of D-glucose transmembrane transport / regulation of nitric-oxide synthase activity / hyaluronan biosynthetic process / positive regulation of T-helper 1 cell cytokine production / positive regulation of complement activation / : / cellular response to interleukin-17 / positive regulation of RNA biosynthetic process / positive regulation of tight junction disassembly / positive regulation of prostaglandin biosynthetic process / negative regulation of gap junction assembly / positive regulation of immature T cell proliferation in thymus / vascular endothelial growth factor production / positive regulation of prostaglandin secretion / positive regulation of neuroinflammatory response / positive regulation of platelet-derived growth factor receptor signaling pathway / regulation of defense response to virus by host / fever generation / positive regulation of fever generation / regulation of establishment of endothelial barrier / CLEC7A/inflammasome pathway / Interleukin-1 processing / negative regulation of synaptic transmission / response to carbohydrate / positive regulation of monocyte chemotactic protein-1 production / interleukin-1 receptor binding / positive regulation of heterotypic cell-cell adhesion / positive regulation of macrophage derived foam cell differentiation / positive regulation of p38MAPK cascade / positive regulation of membrane protein ectodomain proteolysis / positive regulation of vascular endothelial growth factor receptor signaling pathway / positive regulation of granulocyte macrophage colony-stimulating factor production / regulation of canonical NF-kappaB signal transduction / interleukin-1-mediated signaling pathway / response to ATP / Interleukin-10 signaling / positive regulation of cell division / regulation of neurogenesis / positive regulation of vascular endothelial growth factor production / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / negative regulation of MAP kinase activity / Pyroptosis / ectopic germ cell programmed cell death / negative regulation of lipid catabolic process / regulation of ERK1 and ERK2 cascade / Purinergic signaling in leishmaniasis infection / positive regulation of epithelial to mesenchymal transition / positive regulation of T cell proliferation / extrinsic apoptotic signaling pathway in absence of ligand / JNK cascade / positive regulation of glial cell proliferation / neutrophil chemotaxis / embryo implantation / negative regulation of insulin receptor signaling pathway / positive regulation of interleukin-2 production / response to interleukin-1 / positive regulation of mitotic nuclear division / regulation of insulin secretion / secretory granule / positive regulation of protein export from nucleus / cytokine activity / positive regulation of interleukin-8 production / astrocyte activation / positive regulation of JNK cascade / positive regulation of non-canonical NF-kappaB signal transduction / cytokine-mediated signaling pathway / negative regulation of neurogenesis / positive regulation of interleukin-6 production / positive regulation of type II interferon production / Interleukin-1 signaling / cellular response to mechanical stimulus / positive regulation of inflammatory response / positive regulation of angiogenesis / positive regulation of NF-kappaB transcription factor activity / positive regulation of nitric oxide biosynthetic process / integrin binding / cellular response to xenobiotic stimulus / cell-cell signaling / cellular response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / response to lipopolysaccharide / positive regulation of canonical NF-kappaB signal transduction / lysosome / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / positive regulation of MAPK cascade / defense response to Gram-positive bacterium / immune response / positive regulation of cell migration / inflammatory response / protein domain specific binding / negative regulation of cell population proliferation / apoptotic process
Similarity search - Function
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) ...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)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsFinzel, B.C. / Watenpaugh, K.D. / Einspahr, H.M.
Citation
Journal: J.Mol.Biol. / Year: 1989
Title: Crystal structure of recombinant human interleukin-1 beta at 2.0 A resolution.
Authors: Finzel, B.C. / Clancy, L.L. / Holland, D.R. / Muchmore, S.W. / Watenpaugh, K.D. / Einspahr, H.M.
#1: Journal: Proteins: Struct.,Funct.,Genet. / Year: 1988
Title: Crystallization of Purified Recombinant Human Interleukin-1Beta
Authors: Carter, D.B. / Curry, K.A. / Tomich, C.-S.C. / Yem, A.W. / Deibel, M.R. / Tracey, D.E. / Paslay, J.W. / Carter, J.B. / Theriault, N.Y. / Harris, P.K.W. / Reardon, I.M. / Zurcher-Neely, H.A. ...Authors: Carter, D.B. / Curry, K.A. / Tomich, C.-S.C. / Yem, A.W. / Deibel, M.R. / Tracey, D.E. / Paslay, J.W. / Carter, J.B. / Theriault, N.Y. / Harris, P.K.W. / Reardon, I.M. / Zurcher-Neely, H.A. / Heinrikson, R.L. / Clancy, L.L. / Muchmore, S.W. / Watenpaugh, K.D. / Einspahr, H.M.
#2: Journal: J.Cryst.Growth / Year: 1988
Title: Crystallization of Recombinant Human Interleukin 1Beta
Authors: Einspahr, H. / Clancy, L.L. / Muchmore, S.W. / Watenpaugh, K.D. / Harris, P.K.W. / Carter, D.B. / Curry, K.A. / Tomich, C.-S.C. / Yem, A.W. / Deibeljunior, M.R. / Tracey, D.E. / Pasley, J.W. ...Authors: Einspahr, H. / Clancy, L.L. / Muchmore, S.W. / Watenpaugh, K.D. / Harris, P.K.W. / Carter, D.B. / Curry, K.A. / Tomich, C.-S.C. / Yem, A.W. / Deibeljunior, M.R. / Tracey, D.E. / Pasley, J.W. / Staite, N.D. / Carter, J.B. / Theriault, N.Y. / Reardon, I.M. / Zurcher-Neely, H.A. / Heinrikson, R.L.
#3: Journal: Embo J. / Year: 1988
Title: Crystal Structure of the Cytokine Interleukin-1Beta
Authors: Priestle, J.P. / Schaer, H.-P. / Gruetter, M.G.
History
DepositionDec 5, 1989Processing site: BNL
Revision 1.0Jan 15, 1990Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700SHEET THE SHEET PRESENTED AS *BRL* ON SHEET RECORDS BELOW IS ACTUALLY A SIX-STRANDED BETA-BARREL. ...SHEET THE SHEET PRESENTED AS *BRL* ON SHEET RECORDS BELOW IS ACTUALLY A SIX-STRANDED BETA-BARREL. THIS IS REPRESENTED BY A SEVEN-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INTERLEUKIN-1 BETA


Theoretical massNumber of molelcules
Total (without water)17,3961
Polymers17,3961
Non-polymers00
Water1,49583
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.860, 54.860, 77.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
Atom site foot note1: RESIDUE 91 IS A CIS PROLINE.
2: THE SIDE CHAIN ATOMS OF RESIDUES 93 AND 94 ARE DISORDERED AND ARE NOT INCLUDED IN THIS ENTRY.
3: THERE ARE TWO CONFORMATIONS PRESENTED IN THIS ENTRY FOR RESIDUES 63 - 65.

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Components

#1: Protein INTERLEUKIN-1 BETA


Mass: 17395.832 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell: SK-HEP-1 HEMATOMA CELLS / Production host: Escherichia coli (E. coli) / References: UniProt: P01584
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.33 Å3/Da / Density % sol: 63.06 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.2 Mammonium sulfate1reservoir
250 mMpipes1reservoir
31reservoir
41 mMdithiothreitol1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 40 Å / Num. obs: 12333 / % possible obs: 84 % / Num. measured all: 44483 / Rmerge(I) obs: 0.0423

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2→20 Å /
RfactorNum. reflection
obs0.189 12318
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1211 0 0 83 1294
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0250.03
X-RAY DIFFRACTIONp_angle_d0.0470.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0420.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.3181.5
X-RAY DIFFRACTIONp_mcangle_it2.2723
X-RAY DIFFRACTIONp_scbond_it2.0532
X-RAY DIFFRACTIONp_scangle_it3.2424
X-RAY DIFFRACTIONp_plane_restr0.020.03
X-RAY DIFFRACTIONp_chiral_restr0.30.3
X-RAY DIFFRACTIONp_singtor_nbd0.20.4
X-RAY DIFFRACTIONp_multtor_nbd0.2430.4
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2170.4
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.189
Solvent computation
*PLUS
Displacement parameters
*PLUS

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