7z4k - Revision history

OCA at 19:00, 7 September 2022

OCA — Wed, 07 Sep 2022 19:00:59 GMT

←Older revision		Revision as of 19:00, 7 September 2022
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	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/CAS9_STRP1 CAS9_STRP1]] CRISPR (clustered regularly interspaced short palindromic repeat) is an adaptive immune system that provides protection against mobile genetic elements (viruses, transposable elements and conjugative plasmids). CRISPR clusters contain spacers, sequences complementary to antecedent mobile elements, and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA) (Probable). In type II CRISPR systems correct processing of pre-crRNA requires a trans-encoded small RNA (tracrRNA), endogenous ribonuclease 3 (rnc) and this protein. The tracrRNA serves as a guide for ribonuclease 3-aided processing of pre-crRNA. Subsequently Cas9/crRNA/tracrRNA endonucleolytically cleaves linear or circular dsDNA target complementary to the spacer. The target strand not complementary to crRNA is first cut endonucleolytically, then trimmed by 3'-5' exonucleolytically. DNA-binding requires protein and both RNA species. Cas9 probably recognizes a short motif in the CRISPR repeat sequences (the PAM or protospacer adjacent motif) to help distinguish self versus nonself.<ref>PMID:21455174</ref> <ref>PMID:22745249</ref>		[[https://www.uniprot.org/uniprot/CAS9_STRP1 CAS9_STRP1]] CRISPR (clustered regularly interspaced short palindromic repeat) is an adaptive immune system that provides protection against mobile genetic elements (viruses, transposable elements and conjugative plasmids). CRISPR clusters contain spacers, sequences complementary to antecedent mobile elements, and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA) (Probable). In type II CRISPR systems correct processing of pre-crRNA requires a trans-encoded small RNA (tracrRNA), endogenous ribonuclease 3 (rnc) and this protein. The tracrRNA serves as a guide for ribonuclease 3-aided processing of pre-crRNA. Subsequently Cas9/crRNA/tracrRNA endonucleolytically cleaves linear or circular dsDNA target complementary to the spacer. The target strand not complementary to crRNA is first cut endonucleolytically, then trimmed by 3'-5' exonucleolytically. DNA-binding requires protein and both RNA species. Cas9 probably recognizes a short motif in the CRISPR repeat sequences (the PAM or protospacer adjacent motif) to help distinguish self versus nonself.<ref>PMID:21455174</ref> <ref>PMID:22745249</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Cas9 is a CRISPR-associated endonuclease capable of RNA-guided, site-specific DNA cleavage(1-3). The programmable activity of Cas9 has been widely utilized for genome editing applications(4-6), yet its precise mechanisms of target DNA binding and off-target discrimination remain incompletely understood. Here we report a series of cryo-electron microscopy structures of Streptococcus pyogenes Cas9 capturing the directional process of target DNA hybridization. In the early phase of R-loop formation, the Cas9 REC2 and REC3 domains form a positively charged cleft that accommodates the distal end of the target DNA duplex. Guide-target hybridization past the seed region induces rearrangements of the REC2 and REC3 domains and relocation of the HNH nuclease domain to assume a catalytically incompetent checkpoint conformation. Completion of the guide-target heteroduplex triggers conformational activation of the HNH nuclease domain, enabled by distortion of the guide-target heteroduplex, and complementary REC2 and REC3 domain rearrangements. Together, these results establish a structural framework for target DNA-dependent activation of Cas9 that sheds light on its conformational checkpoint mechanism and may facilitate the development of novel Cas9 variants and guide RNA designs with enhanced specificity and activity.
		+
		+	R-loop formation and conformational activation mechanisms of Cas9.,Pacesa M, Loeff L, Querques I, Muckenfuss LM, Sawicka M, Jinek M Nature. 2022 Sep;609(7925):191-196. doi: 10.1038/s41586-022-05114-0. Epub 2022, Aug 24. PMID:36002571<ref>PMID:36002571</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7z4k" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 16:51, 7 September 2022

OCA — Wed, 07 Sep 2022 16:51:01 GMT

←Older revision		Revision as of 16:51, 7 September 2022
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-	====	+	==SpCas9 bound to 10-nucleotide complementary DNA substrate==
-	<StructureSection load='7z4k' size='340' side='right'caption='[[7z4k]]' scene=''>	+	<StructureSection load='7z4k' size='340' side='right'caption='[[7z4k]], [[Resolution\|resolution]] 3.81Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7z4k]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_pyogenes Streptococcus pyogenes] 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=7Z4K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7Z4K FirstGlance]. <br>
	</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=7z4k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7z4k OCA], [https://pdbe.org/7z4k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7z4k RCSB], [https://www.ebi.ac.uk/pdbsum/7z4k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7z4k ProSAT]</span></td></tr>		</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=7z4k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7z4k OCA], [https://pdbe.org/7z4k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7z4k RCSB], [https://www.ebi.ac.uk/pdbsum/7z4k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7z4k ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/CAS9_STRP1 CAS9_STRP1]] CRISPR (clustered regularly interspaced short palindromic repeat) is an adaptive immune system that provides protection against mobile genetic elements (viruses, transposable elements and conjugative plasmids). CRISPR clusters contain spacers, sequences complementary to antecedent mobile elements, and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA) (Probable). In type II CRISPR systems correct processing of pre-crRNA requires a trans-encoded small RNA (tracrRNA), endogenous ribonuclease 3 (rnc) and this protein. The tracrRNA serves as a guide for ribonuclease 3-aided processing of pre-crRNA. Subsequently Cas9/crRNA/tracrRNA endonucleolytically cleaves linear or circular dsDNA target complementary to the spacer. The target strand not complementary to crRNA is first cut endonucleolytically, then trimmed by 3'-5' exonucleolytically. DNA-binding requires protein and both RNA species. Cas9 probably recognizes a short motif in the CRISPR repeat sequences (the PAM or protospacer adjacent motif) to help distinguish self versus nonself.<ref>PMID:21455174</ref> <ref>PMID:22745249</ref>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Z-disk~~]]	+	[[Category: Streptococcus pyogenes]]
		+	[[Category: Synthetic construct]]
		+	[[Category: Jinek M]]
		+	[[Category: Pacesa M]]

OCA at 06:39, 31 August 2022

OCA — Wed, 31 Aug 2022 06:39:23 GMT

←Older revision		Revision as of 06:39, 31 August 2022
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-	'''Unreleased structure'''

-	~~The entry~~ 7z4k ~~is ON HOLD until Paper Publication~~	+	====
-		+	<StructureSection load='7z4k' size='340' side='right'caption='[[7z4k]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>
-	~~Description~~:	+	</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=7z4k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7z4k OCA], [https://pdbe.org/7z4k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7z4k RCSB], [https://www.ebi.ac.uk/pdbsum/7z4k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7z4k ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Z-disk]]

OCA at 10:07, 23 March 2022

OCA — Wed, 23 Mar 2022 10:07:10 GMT

←Older revision		Revision as of 10:07, 23 March 2022
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7z4k is ON HOLD	+	The entry 7z4k is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "7z4k" [edit=sysop:move=sysop]

OCA — Wed, 09 Mar 2022 05:13:51 GMT

Protected "7z4k" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:13, 9 March 2022

OCA: New page: '''Unreleased structure''' The entry 7z4k is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 09 Mar 2022 05:13:50 GMT

New page: '''Unreleased structure''' The entry 7z4k is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7z4k is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]