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- PDB-1ira: COMPLEX OF THE INTERLEUKIN-1 RECEPTOR WITH THE INTERLEUKIN-1 RECE... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ira | ||||||
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Title | COMPLEX OF THE INTERLEUKIN-1 RECEPTOR WITH THE INTERLEUKIN-1 RECEPTOR ANTAGONIST (IL1RA) | ||||||
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![]() | COMPLEX (CYTOKINE RECEPTOR/ANTAGONIST) / CYTOKINE RECEPTOR / RECEPTOR ANTAGONIST / IMMUNOGLOBULIN FOLD / COMPLEX (CYTOKINE RECEPTOR-ANTAGONIST) / COMPLEX (CYTOKINE RECEPTOR-ANTAGONIST) complex | ||||||
Function / homology | ![]() 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, activating receptor activity / interleukin-1, type I receptor binding / interleukin-1 receptor antagonist activity / positive regulation of neutrophil extravasation / interleukin-1, type II receptor binding / interleukin-1 receptor activity / negative regulation of interleukin-1-mediated signaling pathway ...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, activating receptor activity / interleukin-1, type I receptor binding / interleukin-1 receptor antagonist activity / positive regulation of neutrophil extravasation / interleukin-1, type II receptor binding / interleukin-1 receptor activity / negative regulation of interleukin-1-mediated signaling pathway / interleukin-1 binding / positive regulation of T-helper 1 cell cytokine production / negative regulation of heterotypic cell-cell adhesion / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleosidase activity / NAD+ nucleotidase, cyclic ADP-ribose generating / platelet-derived growth factor receptor binding / interleukin-1 receptor binding / inflammatory response to antigenic stimulus / insulin secretion / interleukin-1-mediated signaling pathway / Interleukin-10 signaling / response to glucocorticoid / response to interleukin-1 / cytokine activity / acute-phase response / lipid metabolic process / Interleukin-1 signaling / transmembrane signaling receptor activity / positive regulation of type II interferon production / regulation of inflammatory response / protease binding / Potential therapeutics for SARS / cell surface receptor signaling pathway / inflammatory response / immune response / external side of plasma membrane / centrosome / extracellular space / extracellular exosome / extracellular region / nucleoplasm / membrane / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Schreuder, H.A. / Tardif, C. / Tramp-Kalmeyer, S. / Soffientini, A. / Sarubbi, E. / Akeson, A. / Bowlin, T. / Yanofsky, S. / Barrett, R.W. | ||||||
![]() | ![]() 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: ![]() 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: ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 104.5 KB | Display | ![]() |
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PDB format | ![]() | 82.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 448.7 KB | Display | ![]() |
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Full document | ![]() | 453.6 KB | Display | |
Data in XML | ![]() | 19.2 KB | Display | |
Data in CIF | ![]() | 26.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ilrS ![]() 2cd4 S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 17145.406 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Protein | 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.) ![]() ![]() ![]() | ||
#3: Sugar | ChemComp-NAG / #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54 % | |||||||||||||||
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Crystal grow | Method: 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
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-Data collection
Diffraction | Mean temperature: 296 K |
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Diffraction source | Source: ![]() |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Sep 1, 1994 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→60 Å / Num. obs: 15631 / % possible obs: 97.2 % / Redundancy: 4.7 % / Rsym value: 0.06 |
Reflection shell | Resolution: 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
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Refinement | Method to determine structure: ![]() ![]() Starting model: IL1RA STRUCTURE (PDB ENTRY 1ILR) AND TRUNCATED CD4 DOMAIN (PDB ENTRY 2CD4) Resolution: 2.7→8 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT
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Displacement parameters | Biso mean: 45.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.82 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.393 |