View source for 6jji


==Crystal structure of a two-quartet RNA parallel G-quadruplex complexed with the porphyrin TMPyP4 (1:1)==
<StructureSection load='6jji' size='340' side='right'caption='[[6jji]], [[Resolution|resolution]] 3.10&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[6jji]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudorabies_virus_Ea Pseudorabies virus Ea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JJI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6JJI FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.1&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=POH:(1Z,4Z,9Z,15Z)-5,10,15,20-TETRAKIS(1-METHYLPYRIDIN-1-IUM-4-YL)-21,23-DIHYDROPORPHYRIN'>POH</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=6jji FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jji OCA], [https://pdbe.org/6jji PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6jji RCSB], [https://www.ebi.ac.uk/pdbsum/6jji PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6jji ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Obtaining phase information remains a formidable challenge for nucleic acid structure determination. The introduction of an X-ray synchrotron beamline designed to be tunable to long wavelengths at Diamond Light Source has opened the possibility to native de novo structure determinations by the use of intrinsic scattering elements. This provides opportunities to overcome the limitations of introducing modifying nucleotides, often required to derive phasing information. In this paper, we build on established methods to generate new tools for nucleic acid structure determinations. We report on the use of (i) native intrinsic potassium single-wavelength anomalous dispersion methods (K-SAD), (ii) use of anomalous scattering elements integral to the crystallization buffer (extrinsic cobalt and intrinsic potassium ions), (iii) extrinsic bromine and intrinsic phosphorus SAD to solve complex nucleic acid structures. Using the reported methods we solved the structures of (i) Pseudorabies virus (PRV) RNA G-quadruplex and ligand complex, (ii) PRV DNA G-quadruplex, and (iii) an i-motif of human telomeric sequence. Our results highlight the utility of using intrinsic scattering as a pathway to solve and determine non-canonical nucleic acid motifs and reveal the variability of topology, influence of ligand binding, and glycosidic angle rearrangements seen between RNA and DNA G-quadruplexes of the same sequence.

Native de novo structural determinations of non-canonical nucleic acid motifs by X-ray crystallography at long wavelengths.,Zhang Y, El Omari K, Duman R, Liu S, Haider S, Wagner A, Parkinson GN, Wei D Nucleic Acids Res. 2020 May 26. pii: 5846030. doi: 10.1093/nar/gkaa439. PMID:32453431<ref>PMID:32453431</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 6jji" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Pseudorabies virus Ea]]
[[Category: Parkinson GN]]
[[Category: Wei DG]]
[[Category: Zhang YS]]