8h4u: Difference between revisions

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

~~The entry~~ 8h4u is ~~ON HOLD until Paper~~ Publication

==Cryo-EM structure of a riboendonuclease==

== Structural highlights ==

<table><tr><td colspan='2'>[[8h4u]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermoclostridium_caenicola Thermoclostridium caenicola]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8H4U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8H4U FirstGlance]. <br>

</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.5Å</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=8h4u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8h4u OCA], [https://pdbe.org/8h4u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8h4u RCSB], [https://www.ebi.ac.uk/pdbsum/8h4u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8h4u ProSAT]</span></td></tr>

</table>

== Function ==

[https://www.uniprot.org/uniprot/A0A1M6GDI0_9FIRM A0A1M6GDI0_9FIRM]

== Publication Abstract from PubMed ==

The RNA-targeting type VI CRISPR-Cas effector complexes are widely used in biotechnology applications such as gene knockdown, RNA editing, and molecular diagnostics. Compared with Cas13a from mesophilic organisms, a newly discovered Cas13a from thermophilic bacteria Thermoclostridium caenicola (TccCas13a) shows low sequence similarity, high thermostability, and lacks pre-crRNA processing activity. The thermostability of TccCas13a has been harnessed to make a sensitive and robust tool for nucleic acid detection. Here we present the structures of TccCas13a-crRNA binary complex at 2.8 A, and TccCas13a at 3.5 A. Although TccCas13a shares a similarly bilobed architecture with other mesophilic organism-derived Cas13a proteins, TccCas13a displayed distinct structure features. Specifically, it holds a long crRNA 5'-flank, forming extensive polar contacts with Helical-1 and HEPN2 domains. The detailed analysis of the interaction between crRNA 5'-flank and TccCas13a suggested lack of suitable nucleophile to attack the 2'-OH of crRNA 5'-flank may explain why TccCas13a fails to cleave pre-crRNA. The stem-loop segment of crRNA spacer toggles between double-stranded and single-stranded conformational states, suggesting a potential safeguard mechanism for target recognition. Superimposition of the structures of TccCas13a and TccCas13a-crRNA revealed several conformational changes required for crRNA loading, including dramatic movement of Helical-2 domain. Collectively, these structural insights expand our understanding into type VI CRISPR-Cas effectors, and would facilitate the development of TccCas13a-based applications.

~~Authors:~~ Li, Z., ~~Wang, F~~.

Structural Basis for the Ribonuclease Activity of a Thermostable CRISPR-Cas13a from Thermoclostridium caenicola.,Wang F, Zhang C, Xu H, Zeng W, Ma L, Li Z J Mol Biol. 2023 Sep 1;435(17):168197. doi: 10.1016/j.jmb.2023.168197. Epub 2023 , Jul 11. PMID:37442412<ref>PMID:37442412</ref>

~~Description~~: ~~Cryo-EM structure of a riboendonuclease~~

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

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

</div>

[[Category: Li, Z]]

[[Category: Wang, F]]

== References ==

__TOC__

</StructureSection>

[[Category: Large Structures]]

[[Category: Thermoclostridium caenicola]]

[[Category: Li Z]]

[[Category: Wang F]]

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 8h4u is ON HOLD  until Paper Publication
+==Cryo-EM structure of a riboendonuclease==
+<StructureSection load='8h4u' size='340' side='right'caption='[[8h4u]], [[Resolution|resolution]] 3.50&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[8h4u]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermoclostridium_caenicola Thermoclostridium caenicola]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8H4U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8H4U FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.5&#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=8h4u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8h4u OCA], [https://pdbe.org/8h4u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8h4u RCSB], [https://www.ebi.ac.uk/pdbsum/8h4u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8h4u ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/A0A1M6GDI0_9FIRM A0A1M6GDI0_9FIRM]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The RNA-targeting type VI CRISPR-Cas effector complexes are widely used in biotechnology applications such as gene knockdown, RNA editing, and molecular diagnostics. Compared with Cas13a from mesophilic organisms, a newly discovered Cas13a from thermophilic bacteria Thermoclostridium caenicola (TccCas13a) shows low sequence similarity, high thermostability, and lacks pre-crRNA processing activity. The thermostability of TccCas13a has been harnessed to make a sensitive and robust tool for nucleic acid detection. Here we present the structures of TccCas13a-crRNA binary complex at 2.8 A, and TccCas13a at 3.5 A. Although TccCas13a shares a similarly bilobed architecture with other mesophilic organism-derived Cas13a proteins, TccCas13a displayed distinct structure features. Specifically, it holds a long crRNA 5'-flank, forming extensive polar contacts with Helical-1 and HEPN2 domains. The detailed analysis of the interaction between crRNA 5'-flank and TccCas13a suggested lack of suitable nucleophile to attack the 2'-OH of crRNA 5'-flank may explain why TccCas13a fails to cleave pre-crRNA. The stem-loop segment of crRNA spacer toggles between double-stranded and single-stranded conformational states, suggesting a potential safeguard mechanism for target recognition. Superimposition of the structures of TccCas13a and TccCas13a-crRNA revealed several conformational changes required for crRNA loading, including dramatic movement of Helical-2 domain. Collectively, these structural insights expand our understanding into type VI CRISPR-Cas effectors, and would facilitate the development of TccCas13a-based applications.
-Authors: Li, Z., Wang, F.
+Structural Basis for the Ribonuclease Activity of a Thermostable CRISPR-Cas13a from Thermoclostridium caenicola.,Wang F, Zhang C, Xu H, Zeng W, Ma L, Li Z J Mol Biol. 2023 Sep 1;435(17):168197. doi: 10.1016/j.jmb.2023.168197. Epub 2023 , Jul 11. PMID:37442412<ref>PMID:37442412</ref>
-Description: Cryo-EM structure of a riboendonuclease
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Li, Z]]
+<div class="pdbe-citations 8h4u" style="background-color:#fffaf0;"></div>
-[[Category: Wang, F]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
+[[Category: Thermoclostridium caenicola]]
+[[Category: Li Z]]
+[[Category: Wang F]]