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- PDB-3o4o: Crystal structure of an Interleukin-1 receptor complex -

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Basic information

Entry
Database: PDB / ID: 3o4o
TitleCrystal structure of an Interleukin-1 receptor complex
Components
  • Interleukin-1 betaInterleukin 1 beta
  • Interleukin-1 receptor accessory protein
  • Interleukin-1 receptor type 2
KeywordsIMMUNE SYSTEM / cytokine-receptor complex / Beta-trefoil / Ig-like fold
Function / homology
Function and homology information


interleukin-1, type II, blocking receptor activity / Interleukin-33 signaling / interleukin-33 receptor activity / Interleukin-36 pathway / negative regulation of interleukin-1 alpha production / interleukin-1 receptor activity / negative regulation of interleukin-1-mediated signaling pathway / trans-synaptic signaling by trans-synaptic complex / interleukin-1 binding / Receptor-type tyrosine-protein phosphatases ...interleukin-1, type II, blocking receptor activity / Interleukin-33 signaling / interleukin-33 receptor activity / Interleukin-36 pathway / negative regulation of interleukin-1 alpha production / interleukin-1 receptor activity / negative regulation of interleukin-1-mediated signaling pathway / trans-synaptic signaling by trans-synaptic complex / interleukin-1 binding / Receptor-type tyrosine-protein phosphatases / smooth muscle adaptation / positive regulation of T cell mediated immunity / positive regulation of myosin light chain kinase activity / negative regulation of adiponectin secretion / monocyte aggregation / negative regulation of lipid metabolic process / positive regulation of lipid catabolic process / hyaluronan biosynthetic process / negative regulation of glucose transmembrane transport / synaptic membrane adhesion / regulation of postsynaptic density assembly / positive regulation of cell adhesion molecule production / positive regulation of T-helper 1 cell cytokine production / positive regulation of complement activation / positive regulation of calcidiol 1-monooxygenase activity / cellular response to interleukin-17 / sequestering of triglyceride / positive regulation of RNA biosynthetic process / interleukin-33-mediated signaling pathway / negative regulation of gap junction assembly / positive regulation of prostaglandin secretion / NADP+ nucleosidase activity / positive regulation of prostaglandin biosynthetic process / positive regulation of immature T cell proliferation in thymus / vascular endothelial growth factor production / positive regulation of neuroinflammatory response / positive regulation of interleukin-5 production / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / regulation of defense response to virus by host / positive regulation of interleukin-13 production / fever generation / positive regulation of fever generation / neutrophil activation / CLEC7A/inflammasome pathway / regulation of establishment of endothelial barrier / NAD+ nucleotidase, cyclic ADP-ribose generating / Interleukin-1 processing / response to carbohydrate / interleukin-1 receptor binding / positive regulation of monocyte chemotactic protein-1 production / positive regulation of vascular endothelial growth factor receptor signaling pathway / positive regulation of heterotypic cell-cell adhesion / negative regulation of synaptic transmission / positive regulation of synapse assembly / negative regulation of protein processing / positive regulation of granulocyte macrophage colony-stimulating factor production / regulation of canonical NF-kappaB signal transduction / positive regulation of membrane protein ectodomain proteolysis / interleukin-1-mediated signaling pathway / positive regulation of p38MAPK cascade / : / regulation of nitric-oxide synthase activity / response to ATP / positive regulation of interleukin-4 production / macrophage chemotaxis / Interleukin-10 signaling / regulation of insulin secretion / positive regulation of cell division / regulation of presynapse assembly / regulation of neurogenesis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of vascular endothelial growth factor production / negative regulation of cytokine production involved in inflammatory response / ectopic germ cell programmed cell death / Pyroptosis / negative regulation of lipid catabolic process / coreceptor activity / Purinergic signaling in leishmaniasis infection / positive regulation of epithelial to mesenchymal transition / positive regulation of T cell proliferation / JNK cascade / positive regulation of glial cell proliferation / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of interleukin-2 production / embryo implantation / negative regulation of insulin receptor signaling pathway / response to interleukin-1 / positive regulation of mitotic nuclear division / neutrophil chemotaxis / regulation of ERK1 and ERK2 cascade / positive regulation of protein export from nucleus / negative regulation of MAP kinase activity / secretory granule / cytokine activity / astrocyte activation / positive regulation of interleukin-8 production / positive regulation of JNK cascade / positive regulation of MAP kinase activity / protein processing / positive regulation of DNA-binding transcription factor activity
Similarity search - Function
Interleukin-1 receptor type II / 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 II / 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 / TIR domain / Cytokine IL1/FGF / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Interleukin-1 beta / Interleukin-1 receptor type 2 / Interleukin-1 receptor accessory protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsWang, X.Q. / Wang, D.L. / Zhang, S.Y. / Li, L. / Liu, X. / Mei, K.R.
CitationJournal: Nat.Immunol. / Year: 2010
Title: Structural insights into the assembly and activation of IL-1beta with its receptors
Authors: Wang, D.L. / Zhang, S.Y. / Li, L. / Liu, X. / Mei, K.R. / Wang, X.Q.
History
DepositionJul 27, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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
C: Interleukin-1 receptor type 2
B: Interleukin-1 receptor accessory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,7459
Polymers96,0113
Non-polymers1,7346
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6330 Å2
ΔGint-19 kcal/mol
Surface area40670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.830, 177.470, 180.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsAUTHOR STATES THAT THE BIOLOGICAL ASSEMBLY IS UNKNOWN.

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Components

#1: Protein Interleukin-1 beta / Interleukin 1 beta / IL-1beta / IL-1 beta / Catabolin


Mass: 17807.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01584
#2: Protein Interleukin-1 receptor type 2 / IL-1RII / IL-1RT-2 / IL-1RT2 / IL-1R-2 / Interleukin-1 receptor type II / Interleukin-1 receptor ...IL-1RII / IL-1RT-2 / IL-1RT2 / IL-1R-2 / Interleukin-1 receptor type II / Interleukin-1 receptor beta / IL-1R-beta / CD121 antigen-like family member B / CDw121b


Mass: 38945.090 Da / Num. of mol.: 1 / Fragment: IL-1RII ectodomain, residues 14-343
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P27930
#3: Protein Interleukin-1 receptor accessory protein / IL-1RAcP / IL-1 receptor accessory protein / Interleukin-1 receptor 3 / IL-1R-3 / IL-1R3


Mass: 39258.637 Da / Num. of mol.: 1 / Fragment: IL-1RAcP ectodomain, residues 21-350
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9NPH3
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.74 Å3/Da / Density % sol: 67.13 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 17% PEG 10000, 0.1M Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 15, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→43 Å / Num. all: 22700 / Num. obs: 22655 / % possible obs: 99.8 % / Observed criterion σ(F): 1.4 / Observed criterion σ(I): 2.4
Reflection shellResolution: 3.3→3.48 Å / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASESphasing
PHENIX(phenix.refine)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2I1B

2i1b


Resolution: 3.3→36.585 Å / SU ML: 0.02 / σ(F): 1.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2892 1101 5.13 %random
Rwork0.2515 ---
obs0.2534 21443 94.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 70.256 Å2 / ksol: 0.287 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--20.5963 Å2-0 Å2-0 Å2
2---22.6251 Å20 Å2
3----20.5156 Å2
Refinement stepCycle: LAST / Resolution: 3.3→36.585 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6394 0 112 0 6506
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0126877
X-RAY DIFFRACTIONf_angle_d1.129262
X-RAY DIFFRACTIONf_dihedral_angle_d26.3354061
X-RAY DIFFRACTIONf_chiral_restr0.0691022
X-RAY DIFFRACTIONf_plane_restr0.0061146
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3003-3.45040.3283850.31471590X-RAY DIFFRACTION60
3.4504-3.63220.32731480.2872563X-RAY DIFFRACTION99
3.6322-3.85950.28551340.26042631X-RAY DIFFRACTION100
3.8595-4.15720.30171260.25712694X-RAY DIFFRACTION100
4.1572-4.57480.25781510.20582649X-RAY DIFFRACTION100
4.5748-5.23510.24891460.19862664X-RAY DIFFRACTION100
5.2351-6.58940.26741510.24612721X-RAY DIFFRACTION100
6.5894-36.58690.32831600.27772830X-RAY DIFFRACTION99

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