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- PDB-5i1b: A COMPARISON OF THE HIGH RESOLUTION STRUCTURES OF HUMAN AND MURIN... -

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Basic information

Entry
Database: PDB / ID: 5i1b
TitleA COMPARISON OF THE HIGH RESOLUTION STRUCTURES OF HUMAN AND MURINE INTERLEUKIN-1B
ComponentsINTERLEUKIN-1 BETA
KeywordsCYTOKINE
Function / homology
Function and homology information


positive regulation of cell adhesion molecule production / positive regulation of T cell mediated immunity / negative regulation of adiponectin secretion / monocyte aggregation / negative regulation of lipid metabolic process / smooth muscle adaptation / positive regulation of lipid catabolic process / regulation of nitric-oxide synthase activity / negative regulation of D-glucose transmembrane transport / positive regulation of T-helper 1 cell cytokine production ...positive regulation of cell adhesion molecule production / positive regulation of T cell mediated immunity / negative regulation of adiponectin secretion / monocyte aggregation / negative regulation of lipid metabolic process / smooth muscle adaptation / positive regulation of lipid catabolic process / regulation of nitric-oxide synthase activity / negative regulation of D-glucose transmembrane transport / positive regulation of T-helper 1 cell cytokine production / hyaluronan biosynthetic process / 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 prostaglandin secretion / positive regulation of immature T cell proliferation in thymus / vascular endothelial growth factor production / positive regulation of fever generation / positive regulation of platelet-derived growth factor receptor signaling pathway / regulation of defense response to virus by host / fever generation / regulation of establishment of endothelial barrier / CLEC7A/inflammasome pathway / Interleukin-1 processing / response to carbohydrate / positive regulation of heterotypic cell-cell adhesion / positive regulation of monocyte chemotactic protein-1 production / positive regulation of macrophage derived foam cell differentiation / positive regulation of p38MAPK cascade / interleukin-1 receptor binding / negative regulation of synaptic transmission / positive regulation of granulocyte macrophage colony-stimulating factor production / positive regulation of membrane protein ectodomain proteolysis / positive regulation of vascular endothelial growth factor receptor signaling pathway / regulation of canonical NF-kappaB signal transduction / positive regulation of neuroinflammatory response / interleukin-1-mediated signaling pathway / response to ATP / Interleukin-10 signaling / positive regulation of cell division / positive regulation of glial cell proliferation / positive regulation of vascular endothelial growth factor production / Pyroptosis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / regulation of neurogenesis / positive regulation of epithelial to mesenchymal transition / negative regulation of lipid catabolic process / ectopic germ cell programmed cell death / regulation of ERK1 and ERK2 cascade / Purinergic signaling in leishmaniasis infection / negative regulation of MAPK cascade / JNK cascade / extrinsic apoptotic signaling pathway in absence of ligand / neutrophil chemotaxis / positive regulation of mitotic nuclear division / astrocyte activation / regulation of insulin secretion / embryo implantation / negative regulation of insulin receptor signaling pathway / positive regulation of interleukin-2 production / positive regulation of T cell proliferation / response to interleukin-1 / secretory granule / cytokine activity / positive regulation of protein export from nucleus / positive regulation of interleukin-8 production / cellular response to mechanical stimulus / positive regulation of non-canonical NF-kappaB signal transduction / negative regulation of neurogenesis / positive regulation of JNK cascade / positive regulation of interleukin-6 production / integrin binding / cellular response to xenobiotic stimulus / positive regulation of type II interferon production / cytokine-mediated signaling pathway / Interleukin-1 signaling / positive regulation of angiogenesis / positive regulation of nitric oxide biosynthetic process / positive regulation of inflammatory response / cell-cell signaling / cellular response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / response to lipopolysaccharide / positive regulation of canonical NF-kappaB signal transduction / positive regulation of ERK1 and ERK2 cascade / lysosome / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of MAPK cascade / positive regulation of cell migration / defense response to Gram-positive bacterium / immune response / inflammatory response / protein domain specific binding / negative regulation of cell population proliferation / apoptotic process / positive regulation of cell population proliferation / positive regulation of gene expression
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: 2.1 Å
AuthorsOhlendorf, D.H. / Salemme, F.R.
CitationJournal: To be Published
Title: A Comparison of the High Resolution Structures of Human and Murine Interleukin-1B
Authors: Ohlendorf, D.H. / Treharne, A.C. / Weber, P.C. / Wendoloski, J.J. / Salemme, F.R. / Lischwe, M. / Newton, R.C.
History
DepositionSep 7, 1990Processing site: BNL
Revision 1.0Jan 15, 1992Provider: repository / Type: Initial release
Revision 1.1Mar 25, 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 1.4Mar 6, 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 ARRANGEMENT OF THE STRANDS IN IL-1 MAKES A SHEET DESIGNATION MEANINGLESS. THE 12 STRANDS ...SHEET THE ARRANGEMENT OF THE STRANDS IN IL-1 MAKES A SHEET DESIGNATION MEANINGLESS. THE 12 STRANDS HAVE BEEN PRESENTED AS 12 SHEETS OF ONE STRAND EACH ON THE SHEET RECORDS BELOW. THE FIRST GROUP OF FOUR STRANDS ARE PART OF MOTIF A. THE SECOND GROUP OF FOUR STRANDS ARE PART OF MOTIF B. THE THIRD GROUP OF FOUR STRANDS ARE PART OF MOTIF C.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: INTERLEUKIN-1 BETA


Theoretical massNumber of molelcules
Total (without water)17,3961
Polymers17,3961
Non-polymers00
Water1,802100
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.840, 54.840, 76.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
Atom site foot note1: WATERS 201 AND 210, 202 AND 204 COORDINATE THE INTERSECTIONS OF THREE BETA STRANDS.
2: THE SIDE CHAINS OF RESIDUES GLN 14, LEU 69, AND SER 84 WERE MODELED IN TWO CONFORMATIONS OF EQUAL OCCUPANCY.
3: THE DENSITY OF RESIDUE VAL 40 IS CONSISTENT WITH ALL THREE ROTAMERS. IT IS MODELED IN THREE CONFORMATIONS OF EQUAL OCCUPANCY.
4: RESIDUE PRO 91 IS A CIS PROLINE.
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.50478, -0.44759, 0.73815), (0.48778, 0.5576, 0.67168), (-0.71223, 0.6991, -0.06314)28.176, -1.533, 1.55
2given(-0.50478, 0.48778, -0.71223), (-0.44759, 0.5576, 0.6991), (0.73815, 0.67168, -0.06314)16.075, 12.382, -19.671

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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) / References: UniProt: P01584
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE MOLECULE CAN BE DIVIDED INTO THREE SIMILAR MOTIFS, (RESIDUES 1 - 55, RESIDUES 56 - 107, AND ...THE MOLECULE CAN BE DIVIDED INTO THREE SIMILAR MOTIFS, (RESIDUES 1 - 55, RESIDUES 56 - 107, AND RESIDUES 108 - 153). THESE MOTIFS ARE RELATED BY LOCAL THREE FOLD. MTRIX 1 ROTATES MOTIFS ABC ONTO BCA. MTRIX 2 ROTATES MOTIFS ABC ONTO CAB.
Nonpolymer detailsWATERS 201 AND 210, 202 AND 204 COORDINATE THE INTERSECTIONS OF THREE BETA STRANDS.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.32 Å3/Da / Density % sol: 62.9 %

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.1→5 Å / Rfactor obs: 0.173
Refinement stepCycle: LAST / Resolution: 2.1→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1219 0 0 100 1319
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.020.03
X-RAY DIFFRACTIONp_angle_d0.0350.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0330.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr0.0160.03
X-RAY DIFFRACTIONp_chiral_restr0.2660.3
X-RAY DIFFRACTIONp_singtor_nbd0.2010.5
X-RAY DIFFRACTIONp_multtor_nbd0.2380.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.210.5
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

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