8isz - Revision history

OCA at 08:22, 7 February 2024

2024-02-07T08:22:39Z

←Older revision		Revision as of 08:22, 7 February 2024
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	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/A0A1I7NFD7_9BACT A0A1I7NFD7_9BACT]		[https://www.uniprot.org/uniprot/A0A1I7NFD7_9BACT A0A1I7NFD7_9BACT]
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Argonaute (Ago) mediates RNA or DNA guided inhibition of nucleic acids(1,2). Although the mechanisms underlying eukaryotic (eAgos) and long prokaryotic Ago (pAgos) proteins are known, that of short pAgos remains elusive. Here, we determined cryo-EM structures of short pAgo and the associated TIR-APAZ proteins (SPARTA) from Crenotalea thermophila (Crt): a free-state Crt-SPARTA (3.27 A), a guide RNA / target DNA loaded Crt-SPARTA (3.27 A), two Crt-SPARTA dimers with distinct TIR organization (3.49 A and 3.50 A), and a Crt-SPARTA tetramer (3.41 A). These structures reveal that the Crt-SPARTA is composed of a bilobal-fold Ago lobe connecting with a TIR lobe. Whereas the Crt-Ago harbors a MID and a PIWI domains, Crt-TIR-APAZ harbors a TIR, a N-like, a Linker and a Trigger domains. The bound RNA/DNA duplex adopts a B-form conformation that is recognized by base-specific contacts. Nucleic acid binding causes conformational changes because the Trigger acts as a roadblock preventing the guide RNA 5'- and the target DNA 3'-ends from reaching their canonical pockets, which disorders the MID domain and promotes Crt-SPARTA dimerization. Two RNA/DNA-loaded Crt-SPARTA dimers form a tetramer through their TIR domains. Four Crt-TIR assemble into two parallel, head-to-tail TIR organization, indicating a NADase-active conformation, which is supported by our mutagenesis study. Our results reveal the structural basis of short pAgos in defensing invading nucleic acids and provide insights for optimizing SPARTA-based programmable DNA sequences detection.
-
-	Nucleic acid-triggered NADase activation of a short prokaryotic Argonaute.,Gao X, Shang K, Zhu K, Wang L, Mu Z, Fu X, Yu X, Qin B, Zhu H, Ding W, Cui S Nature. 2023 Oct 2. doi: 10.1038/s41586-023-06665-6. PMID:37783228<ref>PMID:37783228</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 8isz" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 14:08, 18 October 2023

2023-10-18T14:08:39Z

←Older revision		Revision as of 14:08, 18 October 2023
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-	'''Unreleased structure'''

-	~~The entry~~ 8isz is ~~ON HOLD until Paper~~ Publication	+	==Structure of procaryotic Ago with DNA-RNA complex==
		+	<StructureSection load='8isz' size='340' side='right'caption='[[8isz]], [[Resolution\|resolution]] 3.27Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[8isz]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermoflavifilum_thermophilum Thermoflavifilum thermophilum] 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=8ISZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8ISZ 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]] 3.27Å</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=8isz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8isz OCA], [https://pdbe.org/8isz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8isz RCSB], [https://www.ebi.ac.uk/pdbsum/8isz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8isz ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A1I7NFD7_9BACT A0A1I7NFD7_9BACT]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Argonaute (Ago) mediates RNA or DNA guided inhibition of nucleic acids(1,2). Although the mechanisms underlying eukaryotic (eAgos) and long prokaryotic Ago (pAgos) proteins are known, that of short pAgos remains elusive. Here, we determined cryo-EM structures of short pAgo and the associated TIR-APAZ proteins (SPARTA) from Crenotalea thermophila (Crt): a free-state Crt-SPARTA (3.27 A), a guide RNA / target DNA loaded Crt-SPARTA (3.27 A), two Crt-SPARTA dimers with distinct TIR organization (3.49 A and 3.50 A), and a Crt-SPARTA tetramer (3.41 A). These structures reveal that the Crt-SPARTA is composed of a bilobal-fold Ago lobe connecting with a TIR lobe. Whereas the Crt-Ago harbors a MID and a PIWI domains, Crt-TIR-APAZ harbors a TIR, a N-like, a Linker and a Trigger domains. The bound RNA/DNA duplex adopts a B-form conformation that is recognized by base-specific contacts. Nucleic acid binding causes conformational changes because the Trigger acts as a roadblock preventing the guide RNA 5'- and the target DNA 3'-ends from reaching their canonical pockets, which disorders the MID domain and promotes Crt-SPARTA dimerization. Two RNA/DNA-loaded Crt-SPARTA dimers form a tetramer through their TIR domains. Four Crt-TIR assemble into two parallel, head-to-tail TIR organization, indicating a NADase-active conformation, which is supported by our mutagenesis study. Our results reveal the structural basis of short pAgos in defensing invading nucleic acids and provide insights for optimizing SPARTA-based programmable DNA sequences detection.

-	~~Authors~~:	+	Nucleic acid-triggered NADase activation of a short prokaryotic Argonaute.,Gao X, Shang K, Zhu K, Wang L, Mu Z, Fu X, Yu X, Qin B, Zhu H, Ding W, Cui S Nature. 2023 Oct 2. doi: 10.1038/s41586-023-06665-6. PMID:37783228<ref>PMID:37783228</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 8isz" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Synthetic construct]]
		+	[[Category: Thermoflavifilum thermophilum]]
		+	[[Category: Cui S]]
		+	[[Category: Ding W]]
		+	[[Category: Gao X]]
		+	[[Category: Shang K]]
		+	[[Category: Zhu H]]

OCA at 11:50, 20 September 2023

2023-09-20T11:50:51Z

←Older revision		Revision as of 11:50, 20 September 2023
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 8isz is ON HOLD	+	The entry 8isz is ON HOLD until Paper Publication

	Authors:		Authors:

OCA at 03:48, 9 August 2023

2023-08-09T03:48:37Z

←Older revision		Revision as of 03:48, 9 August 2023
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 8isz is ON HOLD ~~until Paper Publication~~	+	The entry 8isz is ON HOLD

	Authors:		Authors:

OCA at 05:25, 3 May 2023

2023-05-03T05:25:34Z

←Older revision		Revision as of 05:25, 3 May 2023
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 8isz is ON HOLD	+	The entry 8isz is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "8isz" [edit=sysop:move=sysop]

2023-03-29T05:01:03Z

Protected "8isz" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:01, 29 March 2023

OCA: New page: '''Unreleased structure''' The entry 8isz is ON HOLD Authors: Description: Category: Unreleased Structures

2023-03-29T05:01:02Z

New page: '''Unreleased structure''' The entry 8isz is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 8isz is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]