6ify - Revision history

OCA at 10:33, 27 March 2024

2024-03-27T10:33:14Z

← Older revision		Revision as of 10:33, 27 March 2024
Line 3:		Line 3:
	<SX load='6ify' size='340' side='right' viewer='molstar' caption='[[6ify]], [[Resolution\|resolution]] 3.80Å' scene=''>		<SX load='6ify' size='340' side='right' viewer='molstar' caption='[[6ify]], [[Resolution\|resolution]] 3.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6ify]] is a 10 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_19258 Atcc 19258~~] and [~~http~~://en.wikipedia.org/wiki/~~Strtn Strtn~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IFY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6IFY FirstGlance]. <br>		<table><tr><td colspan='2'>[[6ify]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_thermophilus Streptococcus thermophilus] and [https://en.wikipedia.org/wiki/Streptococcus_thermophilus_ND03 Streptococcus thermophilus ND03]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IFY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6IFY FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>~~</td></tr>		</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution\|Resolution]] 3.8Å</td></tr>
	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>csm2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~767463 STRTN]), csm3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=767463 STRTN]), csm4 ([http~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1308 ATCC 19258]), csm5 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=767463 STRTN])~~</td></tr>		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6ify FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ify OCA], [~~http~~://pdbe.org/6ify PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6ify RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6ify PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6ify ProSAT]</span></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=6ify FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ify OCA], [https://pdbe.org/6ify PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ify RCSB], [https://www.ebi.ac.uk/pdbsum/6ify PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ify ProSAT]</span></td></tr>
	</table>		</table>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	Csm, a type III-A CRISPR-Cas interference complex, is a CRISPR RNA (crRNA)-guided RNase that also possesses target RNA-dependent DNase and cyclic oligoadenylate (cOA) synthetase activities. However, the structural features allowing target RNA-binding-dependent activation of DNA cleavage and cOA generation remain unknown. Here, we report the structure of Csm in complex with crRNA together with structures of cognate or non-cognate target RNA bound Csm complexes. We show that depending on complementarity with the 5' tag of crRNA, the 3' anti-tag region of target RNA binds at two distinct sites of the Csm complex. Importantly, the interaction between the non-complementary anti-tag region of cognate target RNA and Csm1 induces a conformational change at the Csm1 subunit that allosterically activates DNA cleavage and cOA generation. Together, our structural studies provide crucial insights into the mechanistic processes required for crRNA-meditated sequence-specific RNA cleavage, RNA target-dependent non-specific DNA cleavage, and cOA generation.

	Structure Studies of the CRISPR-Csm Complex Reveal Mechanism of Co-transcriptional Interference.,You L, Ma J, Wang J, Artamonova D, Wang M, Liu L, Xiang H, Severinov K, Zhang X, Wang Y Cell. 2018 Nov 26. pii: S0092-8674(18)31451-X. doi: 10.1016/j.cell.2018.10.052. PMID:30503210<ref>PMID:30503210</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 6ify" style="background-color:#fffaf0;"></div>~~
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</SX>		</SX>
	~~[[Category: Atcc 19258]]~~
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: ~~Strtn~~]]		[[Category: Streptococcus thermophilus]]
	[[Category: Ma, J]]		[[Category: Streptococcus thermophilus ND03]]
	[[Category: Wang, J]]		[[Category: Ma J]]
	[[Category: Wang, Y]]		[[Category: Wang J]]
	[[Category: You, L]]		[[Category: Wang Y]]
	[[Category: Zhang, X]]		[[Category: You L]]
	~~[[Category: Crispr-cas system]]~~		[[Category: Zhang X]]
	~~[[Category: Csm complex]]~~
	~~[[Category: Rna binding protein]]~~
	~~[[Category: Type iii-a~~]]

OCA at 01:44, 11 April 2020

2020-04-11T01:44:56Z

← Older revision		Revision as of 01:44, 11 April 2020
Line 3:		Line 3:
	<SX load='6ify' size='340' side='right' viewer='molstar' caption='[[6ify]], [[Resolution\|resolution]] 3.80Å' scene=''>		<SX load='6ify' size='340' side='right' viewer='molstar' caption='[[6ify]], [[Resolution\|resolution]] 3.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6ify]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_19258 Atcc 19258] and [http://en.wikipedia.org/wiki/Strtn Strtn]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IFY OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6IFY FirstGlance]. <br>		<table><tr><td colspan='2'>[[6ify]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_19258 Atcc 19258] and [http://en.wikipedia.org/wiki/Strtn Strtn]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IFY OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6IFY FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">csm2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=767463 STRTN]), csm3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=767463 STRTN]), csm4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1308 ATCC 19258]), csm5 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=767463 STRTN])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">csm2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=767463 STRTN]), csm3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=767463 STRTN]), csm4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1308 ATCC 19258]), csm5 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=767463 STRTN])</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=6ify FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ify OCA], [http://pdbe.org/6ify PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ify RCSB], [http://www.ebi.ac.uk/pdbsum/6ify PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ify ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6ify FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ify OCA], [http://pdbe.org/6ify PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ify RCSB], [http://www.ebi.ac.uk/pdbsum/6ify PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ify ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 22:06, 6 March 2020

2020-03-06T22:06:50Z

← Older revision		Revision as of 22:06, 6 March 2020
Line 1:		Line 1:

	==Type III-A Csm complex, Cryo-EM structure of Csm-CTR1==		==Type III-A Csm complex, Cryo-EM structure of Csm-CTR1==
	<~~StructureSection~~ load='6ify' size='340' side='right' caption='[[6ify]], [[Resolution\|resolution]] 3.80Å' scene=''>		<SX load='6ify' size='340' side='right' viewer='molstar' caption='[[6ify]], [[Resolution\|resolution]] 3.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6ify]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_19258 Atcc 19258] and [http://en.wikipedia.org/wiki/Strtn Strtn]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IFY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6IFY FirstGlance]. <br>		<table><tr><td colspan='2'>[[6ify]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_19258 Atcc 19258] and [http://en.wikipedia.org/wiki/Strtn Strtn]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IFY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6IFY FirstGlance]. <br>
Line 20:		Line 20:
	<references/>		<references/>
	__TOC__		__TOC__
	</~~StructureSection~~>		</SX>
	[[Category: Atcc 19258]]		[[Category: Atcc 19258]]
			[[Category: Large Structures]]
	[[Category: Strtn]]		[[Category: Strtn]]
	[[Category: Ma, J]]		[[Category: Ma, J]]

OCA at 09:04, 19 December 2018

2018-12-19T09:04:47Z

← Older revision		Revision as of 09:04, 19 December 2018
Line 3:		Line 3:
	<StructureSection load='6ify' size='340' side='right' caption='[[6ify]], [[Resolution\|resolution]] 3.80Å' scene=''>		<StructureSection load='6ify' size='340' side='right' caption='[[6ify]], [[Resolution\|resolution]] 3.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6ify]] is a 10 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IFY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6IFY FirstGlance]. <br>		<table><tr><td colspan='2'>[[6ify]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_19258 Atcc 19258] and [http://en.wikipedia.org/wiki/Strtn Strtn]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IFY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6IFY FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
			<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">csm2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=767463 STRTN]), csm3 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=767463 STRTN]), csm4 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1308 ATCC 19258]), csm5 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=767463 STRTN])</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=6ify FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ify OCA], [http://pdbe.org/6ify PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ify RCSB], [http://www.ebi.ac.uk/pdbsum/6ify PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ify ProSAT]</span></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=6ify FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ify OCA], [http://pdbe.org/6ify PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ify RCSB], [http://www.ebi.ac.uk/pdbsum/6ify PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ify ProSAT]</span></td></tr>
	</table>		</table>
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Csm, a type III-A CRISPR-Cas interference complex, is a CRISPR RNA (crRNA)-guided RNase that also possesses target RNA-dependent DNase and cyclic oligoadenylate (cOA) synthetase activities. However, the structural features allowing target RNA-binding-dependent activation of DNA cleavage and cOA generation remain unknown. Here, we report the structure of Csm in complex with crRNA together with structures of cognate or non-cognate target RNA bound Csm complexes. We show that depending on complementarity with the 5' tag of crRNA, the 3' anti-tag region of target RNA binds at two distinct sites of the Csm complex. Importantly, the interaction between the non-complementary anti-tag region of cognate target RNA and Csm1 induces a conformational change at the Csm1 subunit that allosterically activates DNA cleavage and cOA generation. Together, our structural studies provide crucial insights into the mechanistic processes required for crRNA-meditated sequence-specific RNA cleavage, RNA target-dependent non-specific DNA cleavage, and cOA generation.

			Structure Studies of the CRISPR-Csm Complex Reveal Mechanism of Co-transcriptional Interference.,You L, Ma J, Wang J, Artamonova D, Wang M, Liu L, Xiang H, Severinov K, Zhang X, Wang Y Cell. 2018 Nov 26. pii: S0092-8674(18)31451-X. doi: 10.1016/j.cell.2018.10.052. PMID:30503210<ref>PMID:30503210</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 6ify" style="background-color:#fffaf0;"></div>
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
			[[Category: Atcc 19258]]
			[[Category: Strtn]]
	[[Category: Ma, J]]		[[Category: Ma, J]]
	[[Category: Wang, J]]		[[Category: Wang, J]]

OCA at 06:55, 12 December 2018

2018-12-12T06:55:08Z

← Older revision		Revision as of 06:55, 12 December 2018
Line 1:		Line 1:
	~~'''Unreleased structure'''~~

	~~The entry~~ 6ify is ~~ON HOLD until Paper Publication~~		==Type III-A Csm complex, Cryo-EM structure of Csm-CTR1==
			<StructureSection load='6ify' size='340' side='right' caption='[[6ify]], [[Resolution\|resolution]] 3.80Å' scene=''>
	~~Authors~~:		== Structural highlights ==
			<table><tr><td colspan='2'>[[6ify]] is a 10 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IFY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6IFY FirstGlance]. <br>
	~~Description~~:		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	[[Category: ~~Unreleased Structures~~]]		<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=6ify FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ify OCA], [http://pdbe.org/6ify PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ify RCSB], [http://www.ebi.ac.uk/pdbsum/6ify PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ify ProSAT]</span></td></tr>
			</table>
			__TOC__
			</StructureSection>
			[[Category: Ma, J]]
			[[Category: Wang, J]]
			[[Category: Wang, Y]]
			[[Category: You, L]]
			[[Category: Zhang, X]]
			[[Category: Crispr-cas system]]
			[[Category: Csm complex]]
			[[Category: Rna binding protein]]
			[[Category: Type iii-a]]

OCA at 04:19, 24 October 2018

2018-10-24T04:19:02Z

← Older revision		Revision as of 04:19, 24 October 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 6ify is ON HOLD		The entry 6ify is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6ify" [edit=sysop:move=sysop]

2018-09-26T06:24:08Z

Protected "6ify" [edit=sysop:move=sysop]

← Older revision	Revision as of 06:24, 26 September 2018
(No difference)

OCA: New page: '''Unreleased structure''' The entry 6ify is ON HOLD Authors: Description: Category: Unreleased Structures

2018-09-26T06:24:06Z

New page: '''Unreleased structure''' The entry 6ify is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6ify is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]