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- PDB-2i1b: CRYSTALLOGRAPHIC REFINEMENT OF INTERLEUKIN-1 BETA AT 2.0 ANGSTROM... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2i1b | ||||||
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Title | CRYSTALLOGRAPHIC REFINEMENT OF INTERLEUKIN-1 BETA AT 2.0 ANGSTROMS RESOLUTION | ||||||
![]() | INTERLEUKIN-1 BETA | ||||||
![]() | CYTOKINE | ||||||
Function / homology | ![]() 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 / hyaluronan biosynthetic process ...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 / hyaluronan biosynthetic process / 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 / negative regulation of gap junction assembly / 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 neuroinflammatory response / regulation of defense response to virus by host / fever generation / positive regulation of fever generation / CLEC7A/inflammasome pathway / regulation of establishment of endothelial barrier / neutrophil activation / 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 granulocyte macrophage colony-stimulating factor production / positive regulation of membrane protein ectodomain proteolysis / regulation of canonical NF-kappaB signal transduction / interleukin-1-mediated signaling pathway / positive regulation of p38MAPK cascade / response to ATP / : / macrophage chemotaxis / Interleukin-10 signaling / regulation of insulin secretion / positive regulation of cell division / 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 / 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 / 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 / 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 / Interleukin-1 signaling / positive regulation of inflammatory response / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to mechanical stimulus / positive regulation of angiogenesis / positive regulation of interleukin-6 production / positive regulation of nitric oxide biosynthetic process / positive regulation of type II interferon production / cellular response to xenobiotic stimulus / integrin binding / cell-cell signaling / positive regulation of NF-kappaB transcription factor activity / cellular response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / positive regulation of canonical NF-kappaB signal transduction / response to lipopolysaccharide / lysosome / defense response to Gram-positive bacterium / positive regulation of cell migration / inflammatory response / positive regulation of protein phosphorylation / immune response / protein domain specific binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() | ||||||
![]() | Priestle, J.P. / Schaer, H.-P. / Gruetter, M.G. | ||||||
![]() | ![]() Title: Crystallographic refinement of interleukin 1 beta at 2.0 A resolution. Authors: Priestle, J.P. / Schar, H.P. / Grutter, M.G. #1: ![]() Title: The Three-Dimensional Structure of Interleukin-1Beta Authors: Priestle, J.P. / Schaer, H.-P. / Gruetter, M.G. #2: ![]() Title: Crystal Structure of the Cytokine Interleukin-1Beta Authors: Priestle, J.P. / Schaer, H.-P. / Gruetter, M.G. #3: ![]() Title: Crystallization and Preliminary X-Ray Diffraction Studies of Recombinant Human Interleukin-1Beta Authors: Schaer, H.-P. / Priestle, J.P. / Gruetter, M.G. | ||||||
History |
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Remark 700 | SHEET THE SHEET PRESENTED AS * B1* ON SHEET RECORDS BELOW IS ACTUALLY A SIX-STRANDED BETA-BARREL. ...SHEET THE SHEET PRESENTED AS * B1* ON SHEET RECORDS BELOW IS ACTUALLY A SIX-STRANDED BETA-BARREL. THIS IS REPRESENTED BY A SEVEN-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 45.9 KB | Display | ![]() |
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PDB format | ![]() | 32.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 363.2 KB | Display | ![]() |
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Full document | ![]() | 368.7 KB | Display | |
Data in XML | ![]() | 5.5 KB | Display | |
Data in CIF | ![]() | 8.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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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Atom site foot note | 1: POSITIONS OF ALA 1, PRO 2, AND SER 153 ARE QUESTIONABLE. 2: POSITIONS OF THE SIDE CHAINS OF GLN 34, GLU 37, GLN 48, GLU 50, GLU 51, ASN 53, ASP 54, GLU 64, ASP 75, LYS 77, LYS 88, LYS 93, LYS 94, LYS 97, AND GLU 141 ARE QUESTIONABLE. 3: RESIDUE PRO 91 IS A CIS PROLINE. |
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Components
#1: Protein | Mass: 17395.832 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.33 Å3/Da / Density % sol: 63.01 % | |||||||||||||||
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Crystal grow | *PLUS Method: unknown | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 2 Å / Lowest resolution: 6.32 Å / Num. obs: 14926 / Rmerge(I) obs: 0.148 |
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Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2→6 Å / Rfactor obs: 0.172 Details: AUTHORS DECLARE THAT THE POSITIONS OF ALA 1, PRO 2, AND SER 153 ARE QUESTIONABLE. ALSO THE POSITIONS OF THE SIDE CHAINS OF GLN 34, GLU 37, GLN 48, GLU 50, GLU 51, ASN 53, ASP 54, GLU 64, ASP ...Details: AUTHORS DECLARE THAT THE POSITIONS OF ALA 1, PRO 2, AND SER 153 ARE QUESTIONABLE. ALSO THE POSITIONS OF THE SIDE CHAINS OF GLN 34, GLU 37, GLN 48, GLU 50, GLU 51, ASN 53, ASP 54, GLU 64, ASP 75, LYS 77, LYS 88, LYS 93, LYS 94, LYS 97, AND GLU 141 ARE QUESTIONABLE. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→6 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 6 Å / Num. reflection all: 14331 / Rfactor all: 0.172 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |