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2nvh

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Determination of Solvent Content in Cavities in Interleukin-1 Using Experimentally-Phased Electron Density

Structural highlights

2nvh is a 1 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.53Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

IL1B_HUMAN Produced by activated macrophages, IL-1 stimulates thymocyte proliferation by inducing IL-2 release, B-cell maturation and proliferation, and fibroblast growth factor activity. IL-1 proteins are involved in the inflammatory response, being identified as endogenous pyrogens, and are reported to stimulate the release of prostaglandin and collagenase from synovial cells.^[1]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

The extent to which water is present within apolar cavities in proteins remains unclear. In the case of interleukin-1beta (IL-1beta), four independent structures solved by x-ray crystallography indicate that water is not present in the central apolar cavity. In contrast, results from NMR spectroscopy suggest that water has high occupancy within the cavity but is positionally disordered, making it undetectable by standard crystallographic methods. A theoretically based crystallographic-phase refinement technique also suggested that there was the equivalent of two fully occupied water molecules within the apolar cavity. To resolve these discrepancies we sought to obtain an experimentally phased electron density map that was free of possible bias caused by mathematical modeling of the protein or the solvent. By combining native diffraction data with multiple wavelength anomalous data from a platinum derivative, accurate phases were obtained. Using these experimental phases, we estimate that occupancy of the apolar cavity in IL-1beta by solvent is close or equal to zero. Polar cavities in the protein that contain ordered solvent molecules serve as internal controls.

Determination of solvent content in cavities in IL-1beta using experimentally phased electron density.,Quillin ML, Wingfield PT, Matthews BW Proc Natl Acad Sci U S A. 2006 Dec 26;103(52):19749-53. Epub 2006 Dec 18. PMID:17179045^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Van Damme J, De Ley M, Opdenakker G, Billiau A, De Somer P, Van Beeumen J. Homogeneous interferon-inducing 22K factor is related to endogenous pyrogen and interleukin-1. Nature. 1985 Mar 21-27;314(6008):266-8. PMID:3920526
↑ Quillin ML, Wingfield PT, Matthews BW. Determination of solvent content in cavities in IL-1beta using experimentally phased electron density. Proc Natl Acad Sci U S A. 2006 Dec 26;103(52):19749-53. Epub 2006 Dec 18. PMID:17179045

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2nvh"

Categories: Homo sapiens | Large Structures | Matthews BW | Quillin ML

@@ Line 3: / Line 3: @@
 <StructureSection load='2nvh' size='340' side='right'caption='[[2nvh]], [[Resolution|resolution]] 1.53&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2nvh]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NVH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2NVH FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2nvh]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NVH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2NVH FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.53&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">IL1B, IL1F2 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
 <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2nvh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nvh OCA], [https://pdbe.org/2nvh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2nvh RCSB], [https://www.ebi.ac.uk/pdbsum/2nvh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2nvh ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/IL1B_HUMAN IL1B_HUMAN]] Produced by activated macrophages, IL-1 stimulates thymocyte proliferation by inducing IL-2 release, B-cell maturation and proliferation, and fibroblast growth factor activity. IL-1 proteins are involved in the inflammatory response, being identified as endogenous pyrogens, and are reported to stimulate the release of prostaglandin and collagenase from synovial cells.<ref>PMID:3920526</ref>
+[https://www.uniprot.org/uniprot/IL1B_HUMAN IL1B_HUMAN] Produced by activated macrophages, IL-1 stimulates thymocyte proliferation by inducing IL-2 release, B-cell maturation and proliferation, and fibroblast growth factor activity. IL-1 proteins are involved in the inflammatory response, being identified as endogenous pyrogens, and are reported to stimulate the release of prostaglandin and collagenase from synovial cells.<ref>PMID:3920526</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 37: / Line 37: @@
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
 [[Category: Large Structures]]
-[[Category: Matthews, B W]]
+[[Category: Matthews BW]]
-[[Category: Quillin, M L]]
+[[Category: Quillin ML]]
-[[Category: Cytokine]]
-[[Category: Hydration]]
-[[Category: Protein folding]]
-[[Category: Water]]

2nvh

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Current revision

Determination of Solvent Content in Cavities in Interleukin-1 Using Experimentally-Phased Electron Density

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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