5uc6: Difference between revisions

Line 1:

~~'''Unreleased structure'''~~

~~The entry~~ 5uc6 is ~~ON HOLD until Paper~~ Publication

==Structural insights into IL-1 alpha recognition by a naphthyl-modified aptamer that mimics IL-1RI Domain III==

== Structural highlights ==

<table><tr><td colspan='2'>[[5uc6]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UC6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UC6 FirstGlance]. <br>

</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO3:PHOSPHITE+ION'>PO3</scene></td></tr>

<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=85Y:'>85Y</scene>, <scene name='pdbligand=ATD:THYMIDINE-3-PHOSPHATE'>ATD</scene></td></tr>

<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5uc6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uc6 OCA], [http://pdbe.org/5uc6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5uc6 RCSB], [http://www.ebi.ac.uk/pdbsum/5uc6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5uc6 ProSAT]</span></td></tr>

</table>

== Function ==

[[http://www.uniprot.org/uniprot/IL1A_HUMAN IL1A_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.

== Publication Abstract from PubMed ==

IL-1alpha is an essential cytokine that contributes to inflammatory responses and is implicated in various forms of pathogenesis and cancer. Here we report a naphthyl modified DNA aptamer that specifically binds IL-1alpha and inhibits its signaling pathway. By solving the crystal structure of the IL-1alpha/aptamer, we provide a high-resolution structure of this critical cytokine and we reveal its functional interaction interface with high-affinity ligands. The non-helical aptamer, which represents a highly compact nucleic acid structure, contains a wealth of new conformational features, including an unknown form of G-quadruplex. The IL-1alpha/aptamer interface is composed of unusual polar and hydrophobic elements, along with an elaborate hydrogen bonding network that is mediated by sodium ion. IL-1alpha uses the same interface to interact with both the aptamer and its cognate receptor IL-1RI, thereby suggesting a novel route to immunomodulatory therapeutics.The cytokine interleukin 1alpha (IL-1alpha) plays an important role in inflammatory processes. Here the authors use SELEX to generate a modified DNA aptamer which specifically binds IL-1alpha, present the structure of the IL-1alpha/aptamer complex and show that this aptamer inhibits the IL-1alpha signaling pathway.

~~Authors~~:

Structural basis for IL-1alpha recognition by a modified DNA aptamer that specifically inhibits IL-1alpha signaling.,Ren X, Gelinas AD, von Carlowitz I, Janjic N, Pyle AM Nat Commun. 2017 Oct 9;8(1):810. doi: 10.1038/s41467-017-00864-2. PMID:28993621<ref>PMID:28993621</ref>

~~Description~~:

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

[[Category: ~~Unreleased Structures~~]]

</div>

== References ==

__TOC__

</StructureSection>

[[Category: Pyle, A]]

[[Category: Ren, X]]

[[Category: Immune system-dna complex]]

[[Category: Somamer]]

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 5uc6 is ON HOLD  until Paper Publication
+==Structural insights into IL-1 alpha recognition by a naphthyl-modified aptamer that mimics IL-1RI Domain III==
+<StructureSection load='5uc6' size='340' side='right' caption='[[5uc6]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[5uc6]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UC6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UC6 FirstGlance]. <br>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO3:PHOSPHITE+ION'>PO3</scene></td></tr>
+<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=85Y:'>85Y</scene>, <scene name='pdbligand=ATD:THYMIDINE-3-PHOSPHATE'>ATD</scene></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5uc6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uc6 OCA], [http://pdbe.org/5uc6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5uc6 RCSB], [http://www.ebi.ac.uk/pdbsum/5uc6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5uc6 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[[http://www.uniprot.org/uniprot/IL1A_HUMAN IL1A_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.
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+IL-1alpha is an essential cytokine that contributes to inflammatory responses and is implicated in various forms of pathogenesis and cancer. Here we report a naphthyl modified DNA aptamer that specifically binds IL-1alpha and inhibits its signaling pathway. By solving the crystal structure of the IL-1alpha/aptamer, we provide a high-resolution structure of this critical cytokine and we reveal its functional interaction interface with high-affinity ligands. The non-helical aptamer, which represents a highly compact nucleic acid structure, contains a wealth of new conformational features, including an unknown form of G-quadruplex. The IL-1alpha/aptamer interface is composed of unusual polar and hydrophobic elements, along with an elaborate hydrogen bonding network that is mediated by sodium ion. IL-1alpha uses the same interface to interact with both the aptamer and its cognate receptor IL-1RI, thereby suggesting a novel route to immunomodulatory therapeutics.The cytokine interleukin 1alpha (IL-1alpha) plays an important role in inflammatory processes. Here the authors use SELEX to generate a modified DNA aptamer which specifically binds IL-1alpha, present the structure of the IL-1alpha/aptamer complex and show that this aptamer inhibits the IL-1alpha signaling pathway.
-Authors:
+Structural basis for IL-1alpha recognition by a modified DNA aptamer that specifically inhibits IL-1alpha signaling.,Ren X, Gelinas AD, von Carlowitz I, Janjic N, Pyle AM Nat Commun. 2017 Oct 9;8(1):810. doi: 10.1038/s41467-017-00864-2. PMID:28993621<ref>PMID:28993621</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 5uc6" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Pyle, A]]
+[[Category: Ren, X]]
+[[Category: Immune system-dna complex]]
+[[Category: Somamer]]