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- PDB-1itb: TYPE-1 INTERLEUKIN-1 RECEPTOR COMPLEXED WITH INTERLEUKIN-1 BETA -

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Basic information

Entry
Database: PDB / ID: 1itb
TitleTYPE-1 INTERLEUKIN-1 RECEPTOR COMPLEXED WITH INTERLEUKIN-1 BETA
Components
  • INTERLEUKIN-1 BETA
  • TYPE 1 INTERLEUKIN-1 RECEPTOR
KeywordsCOMPLEX (IMMUNOGLOBULIN/RECEPTOR) / IMMUNOGLOBULIN FOLD / TRANSMEMBRANE / GLYCOPROTEIN / RECEPTOR / COMPLEX (IMMUNOGLOBULIN-RECEPTOR) / COMPLEX (IMMUNOGLOBULIN-RECEPTOR) complex
Function / homology
Function and homology information


interleukin-1, type I, activating receptor activity / interleukin-1 receptor activity / interleukin-1 binding / negative regulation of interleukin-1-mediated signaling pathway / positive regulation of T cell mediated immunity / negative regulation of adiponectin secretion / negative regulation of lipid metabolic process / smooth muscle adaptation / negative regulation of D-glucose transmembrane transport / positive regulation of lipid catabolic process ...interleukin-1, type I, activating receptor activity / interleukin-1 receptor activity / interleukin-1 binding / negative regulation of interleukin-1-mediated signaling pathway / positive regulation of T cell mediated immunity / negative regulation of adiponectin secretion / negative regulation of lipid metabolic process / smooth muscle adaptation / negative regulation of D-glucose transmembrane transport / positive regulation of lipid catabolic process / positive regulation of cell adhesion molecule production / regulation of nitric-oxide synthase activity / positive regulation of T-helper 1 cell cytokine production / hyaluronan biosynthetic process / positive regulation of complement activation / positive regulation of RNA biosynthetic process / cellular response to interleukin-17 / monocyte aggregation / positive regulation of tight junction disassembly / positive regulation of prostaglandin secretion / positive regulation of immature T cell proliferation in thymus / negative regulation of gap junction assembly / vascular endothelial growth factor production / positive regulation of prostaglandin biosynthetic process / positive regulation of fever generation / regulation of defense response to virus by host / fever generation / positive regulation of platelet-derived growth factor receptor signaling pathway / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / CASP5-mediated substrate cleavage / CASP4-mediated substrate cleavage / NAD+ nucleosidase activity, cyclic ADP-ribose generating / CLEC7A/inflammasome pathway / regulation of establishment of endothelial barrier / Interleukin-1 processing / positive regulation of granulocyte macrophage colony-stimulating factor production / positive regulation of monocyte chemotactic protein-1 production / positive regulation of glial cell proliferation / positive regulation of macrophage derived foam cell differentiation / positive regulation of p38MAPK cascade / platelet-derived growth factor receptor binding / interleukin-1 receptor binding / negative regulation of synaptic transmission / positive regulation of vascular endothelial growth factor receptor signaling pathway / positive regulation of heterotypic cell-cell adhesion / positive regulation of membrane protein ectodomain proteolysis / regulation of canonical NF-kappaB signal transduction / interleukin-1-mediated signaling pathway / positive regulation of neuroinflammatory response / Interleukin-10 signaling / regulation of insulin secretion / positive regulation of cell division / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of vascular endothelial growth factor production / Pyroptosis / regulation of neurogenesis / regulation of ERK1 and ERK2 cascade / negative regulation of lipid catabolic process / positive regulation of epithelial to mesenchymal transition / embryo implantation / Purinergic signaling in leishmaniasis infection / negative regulation of MAPK cascade / positive regulation of protein export from nucleus / positive regulation of interleukin-2 production / negative regulation of insulin receptor signaling pathway / positive regulation of T cell proliferation / positive regulation of mitotic nuclear division / secretory granule / response to interleukin-1 / cytokine activity / positive regulation of interleukin-8 production / cellular response to xenobiotic stimulus / cellular response to mechanical stimulus / positive regulation of type II interferon production / negative regulation of inflammatory response / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of interleukin-6 production / negative regulation of neurogenesis / positive regulation of JNK cascade / integrin binding / cytokine-mediated signaling pathway / positive regulation of nitric oxide biosynthetic process / positive regulation of angiogenesis / positive regulation of inflammatory response / Interleukin-1 signaling / transmembrane signaling receptor activity / cell-cell signaling / cellular response to lipopolysaccharide / regulation of inflammatory response / response to lipopolysaccharide / protease binding / Interleukin-4 and Interleukin-13 signaling / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Potential therapeutics for SARS / positive regulation of MAPK cascade / positive regulation of ERK1 and ERK2 cascade / positive regulation of canonical NF-kappaB signal transduction / cell surface receptor signaling pathway / lysosome / defense response to Gram-positive bacterium
Similarity search - Function
Interleukin-1 receptor type 1 / Interleukin-1 receptor type I/II / IL-1Ra-like, immunoglobulin domain / Immunoglobulin domain / Interleukin-1 receptor family / Interleukin-1 propeptide / Interleukin-1 propeptide / Interleukin-1 conserved site / Interleukin-1 signature. / Interleukin-1 homologues ...Interleukin-1 receptor type 1 / Interleukin-1 receptor type I/II / IL-1Ra-like, immunoglobulin domain / Immunoglobulin domain / Interleukin-1 receptor family / 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 / TIR domain / Immunoglobulin domain / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Interleukin-1 beta / Interleukin-1 receptor type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.5 Å
AuthorsVigers, G.P.A. / Anderson, L.J. / Caffes, P. / Brandhuber, B.J.
CitationJournal: Nature / Year: 1997
Title: Crystal structure of the type-I interleukin-1 receptor complexed with interleukin-1beta.
Authors: Vigers, G.P. / Anderson, L.J. / Caffes, P. / Brandhuber, B.J.
History
DepositionJan 15, 1997Processing site: BNL
Revision 1.0Feb 4, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INTERLEUKIN-1 BETA
B: TYPE 1 INTERLEUKIN-1 RECEPTOR


Theoretical massNumber of molelcules
Total (without water)53,6192
Polymers53,6192
Non-polymers00
Water43224
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)146.952, 68.452, 65.867
Angle α, β, γ (deg.)90.00, 108.95, 90.00
Int Tables number5
Space group name H-MC121

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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) / Cellular location: SECRETED / Production host: Escherichia coli (E. coli) / References: UniProt: P01584
#2: Protein TYPE 1 INTERLEUKIN-1 RECEPTOR


Mass: 36223.148 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cellular location: CELL SURFACE / Production host: Escherichia coli (E. coli) / References: UniProt: P14778
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.92 Å3/Da / Density % sol: 52 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6
Details: PROTEIN WAS CRYSTALLIZED BY HANGING DROP DIFFUSION AGAINST 2.8M AMMONIUM SULFATE, 100MM MES PH 6.0, vapor diffusion - hanging drop
Crystal grow
*PLUS
Temperature: 0-4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.8 Mammonium salfate1reservoir
2100 mMMES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jul 1, 1995 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→15 Å / Num. obs: 20723 / % possible obs: 96.4 % / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Biso Wilson estimate: 37 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 28
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.104 / Mean I/σ(I) obs: 10.9 / % possible all: 94.9

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementMethod to determine structure: MIR / Resolution: 2.5→15 Å / Data cutoff high absF: 10000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
Details: BULK SOLVENT CORRECTION WITH SOLDENSITY = 0.40, SOLRAD = 0.25, B = 50
RfactorNum. reflection% reflectionSelection details
Rfree0.325 2061 9.6 %RANDOM
Rwork0.229 ---
obs0.229 20723 96.4 %-
Displacement parametersBiso mean: 53.7 Å2
Refine analyzeLuzzati sigma a obs: 0.44 Å
Refinement stepCycle: LAST / Resolution: 2.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3587 0 0 31 3618
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.98
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.55
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.5528 128 8.9 %
Rwork0.4308 1246 -
obs--95.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.55

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