6z18: Difference between revisions

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<StructureSection load='6z18' size='340' side='right'caption='[[6z18]], [[Resolution|resolution]] 1.81&Aring;' scene=''>
<StructureSection load='6z18' size='340' side='right'caption='[[6z18]], [[Resolution|resolution]] 1.81&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[6z18]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Z18 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6Z18 FirstGlance]. <br>
<table><tr><td colspan='2'>[[6z18]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6Z18 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6Z18 FirstGlance]. <br>
</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=LV2:'>LV2</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]] 1.81&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LV2:[(2~{R},3~{S},4~{R},5~{R})-5-[4-(dimethylamino)-2-oxidanylidene-pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl+dihydrogen+phosphate'>LV2</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=6z18 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6z18 OCA], [https://pdbe.org/6z18 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6z18 RCSB], [https://www.ebi.ac.uk/pdbsum/6z18 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6z18 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=6z18 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6z18 OCA], [https://pdbe.org/6z18 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6z18 RCSB], [https://www.ebi.ac.uk/pdbsum/6z18 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6z18 ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The N4-methylation of cytidine (m4C and m42C) in RNA plays important roles in both bacterial and eukaryotic cells. In this work, we synthesized a series of m4C and m42C modified RNA oligonucleotides, conducted their base pairing and bioactivity studies, and solved three new crystal structures of the RNA duplexes containing these two modifications. Our thermostability and X-ray crystallography studies, together with the molecular dynamic simulation studies, demonstrated that m4C retains a regular C:G base pairing pattern in RNA duplex and has a relatively small effect on its base pairing stability and specificity. By contrast, the m42C modification disrupts the C:G pair and significantly decreases the duplex stability through a conformational shift of native Watson-Crick pair to a wobble-like pattern with the formation of two hydrogen bonds. This double-methylated m42C also results in the loss of base pairing discrimination between C:G and other mismatched pairs like C:A, C:T and C:C. The biochemical investigation of these two modified residues in the reverse transcription model shows that both mono- or di-methylated cytosine bases could specify the C:T pair and induce the G to T mutation using HIV-1 RT. In the presence of other reverse transcriptases with higher fidelity like AMV-RT, the methylation could either retain the normal nucleotide incorporation or completely inhibit the DNA synthesis. These results indicate the methylation at N4-position of cytidine is a molecular mechanism to fine tune base pairing specificity and affect the coding efficiency and fidelity during gene replication.
Base pairing, structural and functional insights into N4-methylcytidine (m4C) and N4,N4-dimethylcytidine (m42C) modified RNA.,Mao S, Sekula B, Ruszkowski M, Ranganathan SV, Haruehanroengra P, Wu Y, Shen F, Sheng J Nucleic Acids Res. 2020 Oct 9;48(18):10087-10100. doi: 10.1093/nar/gkaa737. PMID:32941619<ref>PMID:32941619</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 6z18" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Haruehanroengra, P]]
[[Category: Synthetic construct]]
[[Category: Mao, S]]
[[Category: Haruehanroengra P]]
[[Category: Ruszkowski, M]]
[[Category: Mao S]]
[[Category: Sekula, B]]
[[Category: Ruszkowski M]]
[[Category: Sheng, J]]
[[Category: Sekula B]]
[[Category: N4]]
[[Category: Sheng J]]
[[Category: N4-dimethylcytidine]]
[[Category: Rna]]
[[Category: Rna duplex 10mer]]

Latest revision as of 07:40, 1 May 2024

Crystal structure of RNA-10mer: CCGG(N4,N4-dimethyl-C)GCCGG; R32 form

6z18, resolution 1.81Å

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