7y7p: Difference between revisions

Line 1:

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

~~The entry~~ 7y7p is ~~ON HOLD until Paper~~ Publication

==QDE-1 in complex with RNA template, RNA primer and AMPNPP==

== Structural highlights ==

<table><tr><td colspan='2'>[[7y7p]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Neurospora_crassa Neurospora crassa] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7Y7P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7Y7P FirstGlance]. <br>

</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=ZAN:5-O-[(S)-HYDROXY{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]ADENOSINE'>ZAN</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=7y7p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7y7p OCA], [https://pdbe.org/7y7p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7y7p RCSB], [https://www.ebi.ac.uk/pdbsum/7y7p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7y7p ProSAT]</span></td></tr>

</table>

== Function ==

[[https://www.uniprot.org/uniprot/Q9Y7G6_NEUCS Q9Y7G6_NEUCS]]

== Publication Abstract from PubMed ==

Neurospora crassa protein QDE-1, a member of the two-barrel polymerase superfamily, possesses both DNA- and RNA-dependent RNA polymerase (DdRP and RdRP) activities. The dual activities are essential for the production of double-stranded RNAs (dsRNAs), the precursors of small interfering RNAs (siRNAs) in N. crassa. Here, we report five complex structures of N-terminal truncated QDE-1 (QDE-1DeltaN), representing four different reaction states: DNA/RNA-templated elongation, the de novo initiation of RNA synthesis, the first step of nucleotide condensation during de novo initiation and initial NTP loading. The template strand is aligned by a bridge-helix and double-psi beta-barrels 2 (DPBB2), the RNA product is held by DPBB1 and the slab domain. The DNA template unpairs with the RNA product at position -7, but the RNA template remains paired. The NTP analog coordinates with cations and is precisely positioned at the addition site by a rigid trigger loop and a proline-containing loop in the active center. The unique C-terminal tail from the QDE-1 dimer partner inserts into the substrate-binding cleft and plays regulatory roles in RNA synthesis. Collectively, this work elucidates the conserved mechanisms for DNA/RNA-dependent dual activities by QDE-1 and other two-barrel polymerase superfamily members.

~~Authors~~:

Structural insights into the dual activities of the two-barrel RNA polymerase QDE-1.,Cui R, Li H, Zhao J, Li X, Gan J, Ma J Nucleic Acids Res. 2022 Sep 23;50(17):10169-10186. doi: 10.1093/nar/gkac727. PMID:36039765<ref>PMID:36039765</ref>

~~Description~~:

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

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

</div>

== References ==

__TOC__

</StructureSection>

[[Category: Large Structures]]

[[Category: Neurospora crassa]]

[[Category: Synthetic construct]]

[[Category: Cui RX]]

[[Category: Gan JH]]

[[Category: Ma JB]]

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 7y7p is ON HOLD  until Paper Publication
+==QDE-1 in complex with RNA template, RNA primer and AMPNPP==
+<StructureSection load='7y7p' size='340' side='right'caption='[[7y7p]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[7y7p]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Neurospora_crassa Neurospora crassa] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7Y7P OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7Y7P FirstGlance]. <br>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=ZAN:5-O-[(S)-HYDROXY{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]AMINO}PHOSPHORYL]ADENOSINE'>ZAN</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=7y7p FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7y7p OCA], [https://pdbe.org/7y7p PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7y7p RCSB], [https://www.ebi.ac.uk/pdbsum/7y7p PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7y7p ProSAT]</span></td></tr>
+</table>
+== Function ==
+[[https://www.uniprot.org/uniprot/Q9Y7G6_NEUCS Q9Y7G6_NEUCS]]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Neurospora crassa protein QDE-1, a member of the two-barrel polymerase superfamily, possesses both DNA- and RNA-dependent RNA polymerase (DdRP and RdRP) activities. The dual activities are essential for the production of double-stranded RNAs (dsRNAs), the precursors of small interfering RNAs (siRNAs) in N. crassa. Here, we report five complex structures of N-terminal truncated QDE-1 (QDE-1DeltaN), representing four different reaction states: DNA/RNA-templated elongation, the de novo initiation of RNA synthesis, the first step of nucleotide condensation during de novo initiation and initial NTP loading. The template strand is aligned by a bridge-helix and double-psi beta-barrels 2 (DPBB2), the RNA product is held by DPBB1 and the slab domain. The DNA template unpairs with the RNA product at position -7, but the RNA template remains paired. The NTP analog coordinates with cations and is precisely positioned at the addition site by a rigid trigger loop and a proline-containing loop in the active center. The unique C-terminal tail from the QDE-1 dimer partner inserts into the substrate-binding cleft and plays regulatory roles in RNA synthesis. Collectively, this work elucidates the conserved mechanisms for DNA/RNA-dependent dual activities by QDE-1 and other two-barrel polymerase superfamily members.
-Authors:
+Structural insights into the dual activities of the two-barrel RNA polymerase QDE-1.,Cui R, Li H, Zhao J, Li X, Gan J, Ma J Nucleic Acids Res. 2022 Sep 23;50(17):10169-10186. doi: 10.1093/nar/gkac727. PMID:36039765<ref>PMID:36039765</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 7y7p" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Neurospora crassa]]
+[[Category: Synthetic construct]]
+[[Category: Cui RX]]
+[[Category: Gan JH]]
+[[Category: Ma JB]]