6pq7

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (07:33, 11 October 2023) (edit) (undo)
 
(One intermediate revision not shown.)
Line 3: Line 3:
<StructureSection load='6pq7' size='340' side='right'caption='[[6pq7]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
<StructureSection load='6pq7' size='340' side='right'caption='[[6pq7]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[6pq7]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PQ7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6PQ7 FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[6pq7]] is a 1 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=6PQ7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6PQ7 FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OXV:~{N}-[2-[2-[2-[2-[2-[2-[(1-methylquinolin-4-yl)methyl]-1,3-benzothiazol-3-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethyl]pentanamide'>OXV</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]] 3&#8491;</td></tr>
-
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[6e8u|6e8u]]</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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OXV:~{N}-[2-[2-[2-[2-[2-[2-[(1-methylquinolin-4-yl)methyl]-1,3-benzothiazol-3-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethyl]pentanamide'>OXV</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=6pq7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pq7 OCA], [http://pdbe.org/6pq7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pq7 RCSB], [http://www.ebi.ac.uk/pdbsum/6pq7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pq7 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=6pq7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pq7 OCA], [https://pdbe.org/6pq7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6pq7 RCSB], [https://www.ebi.ac.uk/pdbsum/6pq7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6pq7 ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
== Publication Abstract from PubMed ==
-
Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics. PHENIX has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms.
+
Turn-on aptamers are in vitro-selected RNAs that bind to conditionally fluorescent small molecules and enhance their fluorescence. Upon binding TO1-biotin, the iMango-III aptamer achieves the largest fluorescence enhancement reported for turn-on aptamers (over 5000-fold). This aptamer was generated by structure-guided engineering and functional reselection of the parental aptamer Mango-III. Structures of both Mango-III and iMango-III have previously been determined by conventional cryocrystallography using synchrotron X-radiation. Using an X-ray free-electron laser (XFEL), the room-temperature iMango-III-TO1-biotin co-crystal structure has now been determined at 3.0 A resolution. This structural model, which was refined against a data set of approximately 1300 diffraction images (each from a single crystal), is largely consistent with the structures determined from single-crystal data sets collected at 100 K. This constitutes a technical benchmark on the way to XFEL pump-probe experiments on fluorescent RNA-small molecule complexes.
-
PHENIX: a comprehensive Python-based system for macromolecular structure solution.,Adams PD, Afonine PV, Bunkoczi G, Chen VB, Davis IW, Echols N, Headd JJ, Hung LW, Kapral GJ, Grosse-Kunstleve RW, McCoy AJ, Moriarty NW, Oeffner R, Read RJ, Richardson DC, Richardson JS, Terwilliger TC, Zwart PH Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):213-21. Epub 2010, Jan 22. PMID:20124702<ref>PMID:20124702</ref>
+
Co-crystal structure of the iMango-III fluorescent RNA aptamer using an X-ray free-electron laser.,Trachman RJ 3rd, Stagno JR, Conrad C, Jones CP, Fischer P, Meents A, Wang YX, Ferre-D'Amare AR Acta Crystallogr F Struct Biol Commun. 2019 Aug 1;75(Pt 8):547-551. doi:, 10.1107/S2053230X19010136. Epub 2019 Aug 2. PMID:31397326<ref>PMID:31397326</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
Line 22: Line 22:
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
-
[[Category: Amare, A R.Ferre-D]]
+
[[Category: Synthetic construct]]
-
[[Category: III, R J.Trachman]]
+
[[Category: Ferre-D'Amare AR]]
-
[[Category: Aptamer]]
+
[[Category: Trachman III RJ]]
-
[[Category: Fluorescent]]
+
-
[[Category: Rna]]
+
-
[[Category: Xfel]]
+

Current revision

Structure of the iMango-III fluorescent aptamer at room temperature.

PDB ID 6pq7

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6pq7"
Personal tools