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- PDB-1ira: COMPLEX OF THE INTERLEUKIN-1 RECEPTOR WITH THE INTERLEUKIN-1 RECE... -

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Entry
Database: PDB / ID: 1ira
TitleCOMPLEX OF THE INTERLEUKIN-1 RECEPTOR WITH THE INTERLEUKIN-1 RECEPTOR ANTAGONIST (IL1RA)
Components
  • INTERLEUKIN-1 RECEPTOR
  • INTERLEUKIN-1 RECEPTOR ANTAGONIST
KeywordsCOMPLEX (CYTOKINE RECEPTOR/ANTAGONIST) / CYTOKINE RECEPTOR / RECEPTOR ANTAGONIST / IMMUNOGLOBULIN FOLD / COMPLEX (CYTOKINE RECEPTOR-ANTAGONIST) / COMPLEX (CYTOKINE RECEPTOR-ANTAGONIST) complex
Function / homology
Function and homology information


interleukin-1 type I receptor antagonist activity / interleukin-1 type II receptor antagonist activity / positive regulation of interleukin-1-mediated signaling pathway / interleukin-1, type I receptor binding / interleukin-1 receptor antagonist activity / interleukin-1, type I, activating receptor activity / positive regulation of neutrophil extravasation / interleukin-1, type II receptor binding / interleukin-1 receptor activity / interleukin-1 binding ...interleukin-1 type I receptor antagonist activity / interleukin-1 type II receptor antagonist activity / positive regulation of interleukin-1-mediated signaling pathway / interleukin-1, type I receptor binding / interleukin-1 receptor antagonist activity / interleukin-1, type I, activating receptor activity / positive regulation of neutrophil extravasation / interleukin-1, type II receptor binding / interleukin-1 receptor activity / interleukin-1 binding / negative regulation of interleukin-1-mediated signaling pathway / smooth muscle adaptation / positive regulation of T-helper 1 cell cytokine production / negative regulation of heterotypic cell-cell adhesion / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / positive regulation of platelet-derived growth factor receptor signaling pathway / NAD+ nucleosidase activity, cyclic ADP-ribose generating / interleukin-1 receptor binding / platelet-derived growth factor receptor binding / interleukin-1-mediated signaling pathway / insulin secretion / Interleukin-10 signaling / response to interleukin-1 / response to glucocorticoid / cytokine activity / acute-phase response / lipid metabolic process / positive regulation of type II interferon production / Interleukin-1 signaling / transmembrane signaling receptor activity / regulation of inflammatory response / protease binding / Potential therapeutics for SARS / cell surface receptor signaling pathway / positive regulation of canonical NF-kappaB signal transduction / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / immune response / inflammatory response / external side of plasma membrane / centrosome / cell surface / extracellular space / extracellular exosome / extracellular region / nucleoplasm / membrane / plasma membrane / cytosol
Similarity search - Function
Interleukin-1 receptor type 1 / Interleukin-1 receptor antagonist/Interleukin-36 / Interleukin-1 receptor type I/II / IL-1Ra-like, immunoglobulin domain / Immunoglobulin domain / Interleukin-1 receptor family / Interleukin-1 conserved site / Interleukin-1 signature. / Interleukin-1 homologues / Interleukin-1 family ...Interleukin-1 receptor type 1 / Interleukin-1 receptor antagonist/Interleukin-36 / Interleukin-1 receptor type I/II / IL-1Ra-like, immunoglobulin domain / Immunoglobulin domain / Interleukin-1 receptor family / Interleukin-1 conserved site / Interleukin-1 signature. / Interleukin-1 homologues / Interleukin-1 family / Interleukin-1 / 18 / TIR domain / Cytokine IL1/FGF / 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 receptor type 1 / Interleukin-1 receptor antagonist protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MIR, MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSchreuder, H.A. / Tardif, C. / Tramp-Kalmeyer, S. / Soffientini, A. / Sarubbi, E. / Akeson, A. / Bowlin, T. / Yanofsky, S. / Barrett, R.W.
Citation
Journal: Nature / Year: 1997
Title: A new cytokine-receptor binding mode revealed by the crystal structure of the IL-1 receptor with an antagonist.
Authors: Schreuder, H. / Tardif, C. / Trump-Kallmeyer, S. / Soffientini, A. / Sarubbi, E. / Akeson, A. / Bowlin, T. / Yanofsky, S. / Barrett, R.W.
#1: Journal: FEBS Lett. / Year: 1995
Title: Crystals of Soluble Interleukin-1 Receptor Complexed with its Natural Antagonist Reveal a 1:1 Receptor-Ligand Complex
Authors: Schreuder, H. / Tardif, C. / Soffientini, A. / Sarubbi, E. / Akeson, A. / Bowlin, T. / Yanofsky, S. / Barrett, R.W.
#2: Journal: Eur.J.Biochem. / Year: 1995
Title: Refined Crystal Structure of the Interleukin-1 Receptor Antagonist. Presence of a Disulfide Link and a Cis-Proline
Authors: Schreuder, H.A. / Rondeau, J.M. / Tardif, C. / Soffientini, A. / Sarubbi, E. / Akeson, A. / Bowlin, T.L. / Yanofsky, S. / Barrett, R.W.
History
DepositionApr 9, 1998Processing site: BNL
Revision 1.0Jun 17, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / 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_leaving_atom_flag / _struct_conn.pdbx_role / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Aug 9, 2023Group: Database references / Refinement description / Structure summary
Category: chem_comp / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: INTERLEUKIN-1 RECEPTOR ANTAGONIST
Y: INTERLEUKIN-1 RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7726
Polymers53,8872
Non-polymers8854
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint6 kcal/mol
Surface area22630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.200, 84.600, 140.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein INTERLEUKIN-1 RECEPTOR ANTAGONIST / IL1RA


Mass: 17145.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: SF9 / Plasmid: TAC-BSP / Production host: Escherichia coli (E. coli) / References: UniProt: P18510
#2: Protein INTERLEUKIN-1 RECEPTOR


Mass: 36741.734 Da / Num. of mol.: 1 / Fragment: TYPE I RECEPTOR, EXTRACELLULAR DOMAINS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: SF9 / Plasmid: PVL1392 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P14778
#3: 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


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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: THE COMPLEX OF THE IL-1 RECEPTOR WITH THE ANTAGONIST WAS PREPARED BY MIXING A SOLUTION OF IL-1 RECEPTOR IN 50 MM TRIS (PH 7.5) AND 150 MM NACL WITH A SOLUTION OF IL1RA IN THE SAME BUFFER. ...Details: THE COMPLEX OF THE IL-1 RECEPTOR WITH THE ANTAGONIST WAS PREPARED BY MIXING A SOLUTION OF IL-1 RECEPTOR IN 50 MM TRIS (PH 7.5) AND 150 MM NACL WITH A SOLUTION OF IL1RA IN THE SAME BUFFER. THE COMPLEX WAS CRYSTALLIZED USING THE HANGING DROP METHOD. THE DROPS WERE PREPARED BY MIXING 4 UL OF THE PROTEIN SOLUTION WITH 1 UL OF RESERVOIR SOLUTION, CONTAINING 30% (W/V) PEG 3350, 400 MM MGCL2 IN 100 MM MOPS BUFFER (PH 7.0)., vapor diffusion - hanging drop
Crystal grow
*PLUS
Temperature: 23 ℃ / pH: 8.8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
113 mg/mlprotein1drop
21.6 Mammonium phosphate1reservoir

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Data collection

DiffractionMean temperature: 296 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE M18X / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Sep 1, 1994 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→60 Å / Num. obs: 15631 / % possible obs: 97.2 % / Redundancy: 4.7 % / Rsym value: 0.06
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.1 % / Rsym value: 0.325 / % possible all: 85.3
Reflection
*PLUS
Num. measured all: 73407 / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
% possible obs: 85.3 % / Rmerge(I) obs: 0.325

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Processing

Software
NameVersionClassification
XDSdata scaling
XSCALEdata scaling
SQUASHphasing
X-PLOR3.1model building
X-PLOR3.1refinement
XDSdata reduction
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR, MOLECULAR REPLACEMENT
Starting model: IL1RA STRUCTURE (PDB ENTRY 1ILR) AND TRUNCATED CD4 DOMAIN (PDB ENTRY 2CD4)

1ilr

2cd4
PDB Unreleased entry


Resolution: 2.7→8 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.314 -9.9 %RANDOM
Rwork0.213 ---
obs0.213 15012 97.6 %-
Displacement parametersBiso mean: 45.2 Å2
Refinement stepCycle: LAST / Resolution: 2.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3638 0 56 86 3780
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.004
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_deg1.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it5.42
X-RAY DIFFRACTIONx_mcangle_it11.54
X-RAY DIFFRACTIONx_scbond_it8.34
X-RAY DIFFRACTIONx_scangle_it17.78
LS refinement shellResolution: 2.7→2.82 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.466 172 9.1 %
Rwork0.393 1463 -
obs--86.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM3_MOD.PROTOPH3.CHO
X-RAY DIFFRACTION3WAT.PARWAT.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.5
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1
LS refinement shell
*PLUS
Rfactor obs: 0.393

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