3p4a: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3p4a]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3P4A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3P4A FirstGlance]. <br>
<table><tr><td colspan='2'>[[3p4a]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3P4A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3P4A FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SR:STRONTIUM+ION'>SR</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]] 1.2&#8491;</td></tr>
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=AF2:2-DEOXY-2-FLUOROADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>AF2</scene>, <scene name='pdbligand=CFZ:2-DEOXY-2-FLUOROCYTIDINE+5-(DIHYDROGEN+PHOSPHATE)'>CFZ</scene>, <scene name='pdbligand=GF2:2-DEOXY-2-FLUOROGUANOSINE+5-(DIHYDROGEN+PHOSPHATE)'>GF2</scene>, <scene name='pdbligand=UFT:2-DEOXY-2-FLUOROURIDINE+5-(DIHYDROGEN+PHOSPHATE)'>UFT</scene></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AF2:2-DEOXY-2-FLUOROADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>AF2</scene>, <scene name='pdbligand=CFZ:2-DEOXY-2-FLUOROCYTIDINE+5-(DIHYDROGEN+PHOSPHATE)'>CFZ</scene>, <scene name='pdbligand=GF2:2-DEOXY-2-FLUOROGUANOSINE+5-(DIHYDROGEN+PHOSPHATE)'>GF2</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SR:STRONTIUM+ION'>SR</scene>, <scene name='pdbligand=UFT:2-DEOXY-2-FLUOROURIDINE+5-(DIHYDROGEN+PHOSPHATE)'>UFT</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=3p4a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3p4a OCA], [https://pdbe.org/3p4a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3p4a RCSB], [https://www.ebi.ac.uk/pdbsum/3p4a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3p4a ProSAT]</span></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=3p4a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3p4a OCA], [https://pdbe.org/3p4a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3p4a RCSB], [https://www.ebi.ac.uk/pdbsum/3p4a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3p4a ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Various chemical modifications are currently being evaluated for improving the efficacy of short interfering RNA (siRNA) duplexes as antisense agents for gene silencing in vivo. Among the 2'-ribose modifications assessed to date, 2'deoxy-2'-fluoro-RNA (2'-F-RNA) has unique properties for RNA interference (RNAi) applications. Thus, 2'-F-modified nucleotides are well tolerated in the guide (antisense) and passenger (sense) siRNA strands and the corresponding duplexes lack immunostimulatory effects, enhance nuclease resistance and display improved efficacy in vitro and in vivo compared with unmodified siRNAs. To identify potential origins of the distinct behaviors of RNA and 2'-F-RNA we carried out thermodynamic and X-ray crystallographic analyses of fully and partially 2'-F-modified RNAs. Surprisingly, we found that the increased pairing affinity of 2'-F-RNA relative to RNA is not, as commonly assumed, the result of a favorable entropic contribution ('conformational preorganization'), but instead primarily based on enthalpy. Crystal structures at high resolution and osmotic stress demonstrate that the 2'-F-RNA duplex is less hydrated than the RNA duplex. The enthalpy-driven, higher stability of the former hints at the possibility that the 2'-substituent, in addition to its important function in sculpting RNA conformation, plays an underappreciated role in modulating Watson-Crick base pairing strength and potentially pi-pi stacking interactions.
Unexpected origins of the enhanced pairing affinity of 2'-fluoro-modified RNA.,Pallan PS, Greene EM, Jicman PA, Pandey RK, Manoharan M, Rozners E, Egli M Nucleic Acids Res. 2010 Dec 22. PMID:21183463<ref>PMID:21183463</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3p4a" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Akinc, A]]
[[Category: Akinc A]]
[[Category: Charisse, K]]
[[Category: Charisse K]]
[[Category: Egli, M]]
[[Category: Egli M]]
[[Category: Greene, E M]]
[[Category: Greene EM]]
[[Category: Hadwiger, P]]
[[Category: Hadwiger P]]
[[Category: John, M]]
[[Category: John M]]
[[Category: Maier, M A]]
[[Category: Maier MA]]
[[Category: Manoharan, M]]
[[Category: Manoharan M]]
[[Category: Mills, K]]
[[Category: Mills K]]
[[Category: Nechev, L]]
[[Category: Nechev L]]
[[Category: Pallan, P S]]
[[Category: Pallan PS]]
[[Category: Pandey, R K]]
[[Category: Pandey RK]]
[[Category: Qin, J]]
[[Category: Qin J]]
[[Category: Rajeev, K G]]
[[Category: Rajeev KG]]
[[Category: Rozners, E]]
[[Category: Rozners E]]
[[Category: 2'-fluoro 2'-deoxyadenosine]]
[[Category: 2'-fluoro 2'-deoxycytidine]]
[[Category: 2'-fluoro 2'-deoxyguanosine]]
[[Category: 2'-fluoro 2'-deoxyuridine]]
[[Category: 2'-fluoro-rna]]
[[Category: O2'-modification]]
[[Category: Octamer]]
[[Category: Rna]]
[[Category: Sirna]]
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