6mj0: Difference between revisions

Latest revision as of 06:32, 11 October 2023

Crystal structure of the complete turnip yellow mosaic virus 3'UTR

Structural highlights

6mj0 is a 2 chain structure with sequence from Turnip yellow mosaic virus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3.1Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Publication Abstract from PubMed

Structured RNA elements, programmed RNA conformational changes, and interactions between different RNA domains underlie many modes of regulating gene expression, mandating studies to understand the foundational principles that govern these phenomena. Exploring the structured 3' untranslated region (UTR) of a viral RNA, we discovered that different contexts of the 3'-UTR confer different abilities to enhance translation of an associated open reading frame. In one context, ribosome-induced conformational changes in a 'sensor' RNA domain affect a separate RNA 'functional' domain, altering translation efficiency. The structure of the entire 3'-UTR reveals that structurally distinct domains use a spine of continuously stacked bases and a strut-like linker to create a conduit for communication within the higher-order architecture. Thus, this 3'-UTR RNA illustrates how RNA can use programmed conformational changes to sense the translation status of an upstream open reading frame, then create a tuned functional response by communicating that information to other RNA elements.

Ribosome-induced RNA conformational changes in a viral 3'-UTR sense and regulate translation levels.,Hartwick EW, Costantino DA, MacFadden A, Nix JC, Tian S, Das R, Kieft JS Nat Commun. 2018 Nov 29;9(1):5074. doi: 10.1038/s41467-018-07542-x. PMID:30498211^[1]

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

References

↑ Hartwick EW, Costantino DA, MacFadden A, Nix JC, Tian S, Das R, Kieft JS. Ribosome-induced RNA conformational changes in a viral 3'-UTR sense and regulate translation levels. Nat Commun. 2018 Nov 29;9(1):5074. doi: 10.1038/s41467-018-07542-x. PMID:30498211 doi:https://dx.doi.org/10.1038/s41467-018-07542-x

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OCA

[1] Hartwick EW, Costantino DA, MacFadden A, Nix JC, Tian S, Das R, Kieft JS. Ribosome-induced RNA conformational changes in a viral 3'-UTR sense and regulate translation levels. Nat Commun. 2018 Nov 29;9(1):5074. doi: 10.1038/s41467-018-07542-x. PMID:30498211 doi:https://dx.doi.org/10.1038/s41467-018-07542-x

[1]

@@ Line 3: / Line 3: @@
 <StructureSection load='6mj0' size='340' side='right'caption='[[6mj0]], [[Resolution|resolution]] 3.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6mj0]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MJ0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6MJ0 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6mj0]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Turnip_yellow_mosaic_virus Turnip yellow mosaic virus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6MJ0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6MJ0 FirstGlance]. <br>
-</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=6mj0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mj0 OCA], [http://pdbe.org/6mj0 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6mj0 RCSB], [http://www.ebi.ac.uk/pdbsum/6mj0 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6mj0 ProSAT]</span></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]] 3.1&#8491;</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=6mj0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6mj0 OCA], [https://pdbe.org/6mj0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6mj0 RCSB], [https://www.ebi.ac.uk/pdbsum/6mj0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6mj0 ProSAT]</span></td></tr>
 </table>
 <div style="background-color:#fffaf0;">
@@ Line 20: / Line 21: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Costantino, D A]]
+[[Category: Turnip yellow mosaic virus]]
-[[Category: Das, R]]
+[[Category: Costantino DA]]
-[[Category: Hartwick, E W]]
+[[Category: Das R]]
-[[Category: Kieft, J S]]
+[[Category: Hartwick EW]]
-[[Category: MacFadden, A]]
+[[Category: Kieft JS]]
-[[Category: Nix, J C]]
+[[Category: MacFadden A]]
-[[Category: Tian, S]]
+[[Category: Nix JC]]
-[[Category: Programmed conformational change]]
+[[Category: Tian S]]
-[[Category: Rna]]
-[[Category: Translation enhancer]]
-[[Category: Trna like-structure]]
-[[Category: Trna mimicry]]

6mj0: Difference between revisions

Latest revision as of 06:32, 11 October 2023

Crystal structure of the complete turnip yellow mosaic virus 3'UTR

Structural highlights

Publication Abstract from PubMed

References

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