7w0e: Difference between revisions

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~~'''Unreleased structure'''~~

The ~~entry 7w0e~~ is ~~ON HOLD~~

==dmDicer2-LoqsPD-dsRNA Active-dicing status==

== Structural highlights ==

<table><tr><td colspan='2'>[[7w0e]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7W0E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7W0E FirstGlance]. <br>

</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=7w0e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7w0e OCA], [https://pdbe.org/7w0e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7w0e RCSB], [https://www.ebi.ac.uk/pdbsum/7w0e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7w0e ProSAT]</span></td></tr>

</table>

== Function ==

[[https://www.uniprot.org/uniprot/A1ZAW0_DROME A1ZAW0_DROME]]

== Publication Abstract from PubMed ==

Small interfering RNAs (siRNAs) are the key components for RNA interference (RNAi), a conserved RNA-silencing mechanism in many eukaryotes(1,2). In Drosophila, an RNase III enzyme Dicer-2 (Dcr-2), aided by its cofactor Loquacious-PD (Loqs-PD), has an important role in generating 21 bp siRNA duplexes from long double-stranded RNAs (dsRNAs)(3,4). ATP hydrolysis by the helicase domain of Dcr-2 is critical to the successful processing of a long dsRNA into consecutive siRNA duplexes(5,6). Here we report the cryo-electron microscopy structures of Dcr-2-Loqs-PD in the apo state and in multiple states in which it is processing a 50 bp dsRNA substrate. The structures elucidated interactions between Dcr-2 and Loqs-PD, and substantial conformational changes of Dcr-2 during a dsRNA-processing cycle. The N-terminal helicase and domain of unknown function 283 (DUF283) domains undergo conformational changes after initial dsRNA binding, forming an ATP-binding pocket and a 5'-phosphate-binding pocket. The overall conformation of Dcr-2-Loqs-PD is relatively rigid during translocating along the dsRNA in the presence of ATP, whereas the interactions between the DUF283 and RIIIDb domains prevent non-specific cleavage during translocation by blocking the access of dsRNA to the RNase active centre. Additional ATP-dependent conformational changes are required to form an active dicing state and precisely cleave the dsRNA into a 21 bp siRNA duplex as confirmed by the structure in the post-dicing state. Collectively, this study revealed the molecular mechanism for the full cycle of ATP-dependent dsRNA processing by Dcr-2-Loqs-PD.

~~Authors~~:

Structural insights into dsRNA processing by Drosophila Dicer-2-Loqs-PD.,Su S, Wang J, Deng T, Yuan X, He J, Liu N, Li X, Huang Y, Wang HW, Ma J Nature. 2022 Jul;607(7918):399-406. doi: 10.1038/s41586-022-04911-x. Epub 2022, Jun 29. PMID:35768513<ref>PMID:35768513</ref>

~~Description~~:

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

[[Category: ~~Unreleased~~ Structures]]

</div>

== References ==

__TOC__

</StructureSection>

[[Category: Drosophila melanogaster]]

[[Category: Large Structures]]

[[Category: Ma J]]

[[Category: Su S]]

[[Category: Wang HW]]

[[Category: Wang J]]

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 7w0e is ON HOLD
+==dmDicer2-LoqsPD-dsRNA Active-dicing status==
+<StructureSection load='7w0e' size='340' side='right'caption='[[7w0e]], [[Resolution|resolution]] 4.03&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[7w0e]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7W0E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7W0E FirstGlance]. <br>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=7w0e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7w0e OCA], [https://pdbe.org/7w0e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7w0e RCSB], [https://www.ebi.ac.uk/pdbsum/7w0e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7w0e ProSAT]</span></td></tr>
+</table>
+== Function ==
+[[https://www.uniprot.org/uniprot/A1ZAW0_DROME A1ZAW0_DROME]]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Small interfering RNAs (siRNAs) are the key components for RNA interference (RNAi), a conserved RNA-silencing mechanism in many eukaryotes(1,2). In Drosophila, an RNase III enzyme Dicer-2 (Dcr-2), aided by its cofactor Loquacious-PD (Loqs-PD), has an important role in generating 21 bp siRNA duplexes from long double-stranded RNAs (dsRNAs)(3,4). ATP hydrolysis by the helicase domain of Dcr-2 is critical to the successful processing of a long dsRNA into consecutive siRNA duplexes(5,6). Here we report the cryo-electron microscopy structures of Dcr-2-Loqs-PD in the apo state and in multiple states in which it is processing a 50 bp dsRNA substrate. The structures elucidated interactions between Dcr-2 and Loqs-PD, and substantial conformational changes of Dcr-2 during a dsRNA-processing cycle. The N-terminal helicase and domain of unknown function 283 (DUF283) domains undergo conformational changes after initial dsRNA binding, forming an ATP-binding pocket and a 5'-phosphate-binding pocket. The overall conformation of Dcr-2-Loqs-PD is relatively rigid during translocating along the dsRNA in the presence of ATP, whereas the interactions between the DUF283 and RIIIDb domains prevent non-specific cleavage during translocation by blocking the access of dsRNA to the RNase active centre. Additional ATP-dependent conformational changes are required to form an active dicing state and precisely cleave the dsRNA into a 21 bp siRNA duplex as confirmed by the structure in the post-dicing state. Collectively, this study revealed the molecular mechanism for the full cycle of ATP-dependent dsRNA processing by Dcr-2-Loqs-PD.
-Authors:
+Structural insights into dsRNA processing by Drosophila Dicer-2-Loqs-PD.,Su S, Wang J, Deng T, Yuan X, He J, Liu N, Li X, Huang Y, Wang HW, Ma J Nature. 2022 Jul;607(7918):399-406. doi: 10.1038/s41586-022-04911-x. Epub 2022, Jun 29. PMID:35768513<ref>PMID:35768513</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 7w0e" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Drosophila melanogaster]]
+[[Category: Large Structures]]
+[[Category: Ma J]]
+[[Category: Su S]]
+[[Category: Wang HW]]
+[[Category: Wang J]]