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- PDB-4dep: Structure of the IL-1b signaling complex -

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Basic information

Entry
Database: PDB / ID: 4dep
TitleStructure of the IL-1b signaling complex
Components
  • Interleukin-1 beta
  • Interleukin-1 receptor accessory protein
  • Interleukin-1 receptor type 1
KeywordsIMMUNE SYSTEM / b-trefoil / immunoglobulin / extracellular
Function / homology
Function and homology information


positive regulation of interleukin-1-mediated signaling pathway / interleukin-1, type I, activating receptor activity / Interleukin-33 signaling / interleukin-33 receptor activity / positive regulation of neutrophil extravasation / Interleukin-36 pathway / interleukin-1 receptor activity / trans-synaptic signaling by trans-synaptic complex / interleukin-1 binding / Receptor-type tyrosine-protein phosphatases ...positive regulation of interleukin-1-mediated signaling pathway / interleukin-1, type I, activating receptor activity / Interleukin-33 signaling / interleukin-33 receptor activity / positive regulation of neutrophil extravasation / Interleukin-36 pathway / interleukin-1 receptor activity / 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 / negative regulation of glucose transmembrane transport / regulation of nitric-oxide synthase activity / regulation of postsynaptic density assembly / hyaluronan biosynthetic process / positive regulation of cell adhesion molecule production / positive regulation of T-helper 1 cell cytokine production / synaptic membrane adhesion / 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 / negative regulation of gap junction assembly / interleukin-33-mediated signaling pathway / positive regulation of prostaglandin secretion / positive regulation of prostaglandin biosynthetic process / positive regulation of immature T cell proliferation in thymus / vascular endothelial growth factor production / positive regulation of interleukin-13 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 / fever generation / NAD+ nucleosidase activity / positive regulation of fever generation / CLEC7A/inflammasome pathway / regulation of establishment of endothelial barrier / neutrophil activation / NAD+ nucleotidase, cyclic ADP-ribose generating / platelet-derived growth factor receptor binding / 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 / positive regulation of membrane protein ectodomain proteolysis / regulation of canonical NF-kappaB signal transduction / positive regulation of granulocyte macrophage colony-stimulating factor production / interleukin-1-mediated signaling pathway / positive regulation of p38MAPK cascade / 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 / 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 / positive regulation of glial cell proliferation / JNK cascade / extrinsic apoptotic signaling pathway in absence of ligand / positive regulation of interleukin-2 production / negative regulation of insulin receptor signaling pathway / embryo implantation / 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 / positive regulation of interleukin-8 production / astrocyte activation / positive regulation of JNK cascade / positive regulation of MAP kinase activity / cytokine-mediated signaling pathway / positive regulation of DNA-binding transcription factor activity / negative regulation of neurogenesis
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 / TIR domain / Cytokine IL1/FGF / Toll - interleukin 1 - resistance / Immunoglobulin domain / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Immunoglobulin domain / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Interleukin-1 beta / Interleukin-1 receptor type 1 / Interleukin-1 receptor accessory protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsThomas, C. / Garcia, K.C.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Structure of the activating IL-1 receptor signaling complex.
Authors: Thomas, C. / Bazan, J.F. / Garcia, K.C.
History
DepositionJan 21, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2012Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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_seq_id / _struct_conn.ptnr1_label_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Interleukin-1 beta
B: Interleukin-1 receptor type 1
C: Interleukin-1 receptor accessory protein
D: Interleukin-1 beta
E: Interleukin-1 receptor type 1
F: Interleukin-1 receptor accessory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,86320
Polymers189,7666
Non-polymers3,09714
Water1267
1
A: Interleukin-1 beta
B: Interleukin-1 receptor type 1
C: Interleukin-1 receptor accessory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,43110
Polymers94,8833
Non-polymers1,5487
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8400 Å2
ΔGint6 kcal/mol
Surface area35150 Å2
MethodPISA
2
D: Interleukin-1 beta
E: Interleukin-1 receptor type 1
F: Interleukin-1 receptor accessory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,43110
Polymers94,8833
Non-polymers1,5487
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9220 Å2
ΔGint8 kcal/mol
Surface area34940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.990, 65.900, 163.400
Angle α, β, γ (deg.)90.00, 90.35, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 17807.289 Da / Num. of mol.: 2 / Fragment: UNP residues 117-269
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL-1b, IL1B, IL1F2 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / References: UniProt: P01584
#2: Protein Interleukin-1 receptor type 1 / IL-1R-1 / IL-1RT-1 / IL-1RT1 / CD121 antigen-like family member A / Interleukin-1 receptor alpha / ...IL-1R-1 / IL-1RT-1 / IL-1RT1 / CD121 antigen-like family member A / Interleukin-1 receptor alpha / IL-1R-alpha / Interleukin-1 receptor type I / p80


Mass: 36967.965 Da / Num. of mol.: 2 / Fragment: UNP residues 18-336
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL-1RI, IL1R, IL1R1, IL1RA, IL1RT1 / Production host: Homo sapiens (human) / References: UniProt: P14778
#3: Protein Interleukin-1 receptor accessory protein / IL-1 receptor accessory protein / IL-1RAcP / Interleukin-1 receptor 3 / IL-1R-3 / IL-1R3


Mass: 40107.699 Da / Num. of mol.: 2 / Fragment: UNP residues 21-367
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C3orf13, IL-1RAcP, IL1R3, IL1RAP / Production host: Homo sapiens (human) / References: UniProt: Q9NPH3
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 14
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O

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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: 3.01 Å3/Da / Density % sol: 59.1 %
Crystal growTemperature: 293 K / pH: 6.5
Details: 12% PEG 5000 MME, 100 mM MES pH 6.5, 12% 1-propanol, protein at 12 mg/mL, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1
DetectorType: ADSC Q315R / Detector: CCD / Date: Sep 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→19.7 Å / Num. obs: 41079 / % possible obs: 96.3 % / Redundancy: 1.7 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 10.5
Reflection shellResolution: 3.1→3.2 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.361 / Mean I/σ(I) obs: 2.2 / % possible all: 98.7

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→19.7 Å / SU ML: 0.95 / σ(F): 1.99 / Phase error: 26.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.277 2055 5 %
Rwork0.21 --
obs0.213 41079 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 21.56 Å2 / ksol: 0.3 e/Å3
Refinement stepCycle: LAST / Resolution: 3.1→19.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11456 0 196 7 11659
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01711971
X-RAY DIFFRACTIONf_angle_d1.52316284
X-RAY DIFFRACTIONf_dihedral_angle_d19.4624281
X-RAY DIFFRACTIONf_chiral_restr0.0921865
X-RAY DIFFRACTIONf_plane_restr0.012070
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.17190.37221370.29112591X-RAY DIFFRACTION100
3.1719-3.25080.32581360.26372591X-RAY DIFFRACTION100
3.2508-3.33830.3491360.24262584X-RAY DIFFRACTION100
3.3383-3.43610.32091370.23642598X-RAY DIFFRACTION100
3.4361-3.54640.2691360.22342597X-RAY DIFFRACTION100
3.5464-3.67230.31411390.21782631X-RAY DIFFRACTION100
3.6723-3.81830.32741350.22022573X-RAY DIFFRACTION100
3.8183-3.99080.3271350.2142567X-RAY DIFFRACTION100
3.9908-4.19920.26471400.19272643X-RAY DIFFRACTION100
4.1992-4.45950.21691370.17652612X-RAY DIFFRACTION100
4.4595-4.79920.24231370.16382604X-RAY DIFFRACTION100
4.7992-5.27380.25561380.18132614X-RAY DIFFRACTION100
5.2738-6.01780.25071380.20522632X-RAY DIFFRACTION99
6.0178-7.51130.25481380.22732626X-RAY DIFFRACTION99
7.5113-19.70510.24511360.222561X-RAY DIFFRACTION94

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