6je9 - Revision history

OCA at 10:07, 22 November 2023

OCA — Wed, 22 Nov 2023 10:07:13 GMT

←Older revision		Revision as of 10:07, 22 November 2023
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	<StructureSection load='6je9' size='340' side='right'caption='[[6je9]], [[Resolution\|resolution]] 3.46Å' scene=''>		<StructureSection load='6je9' size='340' side='right'caption='[[6je9]], [[Resolution\|resolution]] 3.46Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6je9]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Neim8 Neim8~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JE9 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6JE9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6je9]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Neisseria_meningitidis_8013 Neisseria meningitidis 8013] 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=6JE9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6JE9 FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~cas9~~, ~~NMV_1993 (~~[~~http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=604162 NEIM8])~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 3.46Å</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=6je9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6je9 OCA], [~~http~~://pdbe.org/6je9 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6je9 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6je9 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6je9 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=6je9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6je9 OCA], [https://pdbe.org/6je9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6je9 RCSB], [https://www.ebi.ac.uk/pdbsum/6je9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6je9 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/CAS9_NEIM8 CAS9_NEIM8]] 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). In type II CRISPR systems correct processing of pre-crRNA requires a trans-encoded small RNA (tracrRNA), endogenous ribonuclease 3 (rnc) and this protein, although RNase 3 is not required for 5'-processing of crRNA in this strain. Cas9/crRNA/tracrRNA endonucleolytically cleaves linear or circular dsDNA target complementary to the spacer; Cas9 is inactive in the absence of the 2 guide RNAs (gRNA, PubMed:23940360). Cas9 recognizes the protospacer adjacent motif (PAM) in the CRISPR repeat sequences to help distinguish self versus nonself, as targets within the bacterial CRISPR locus do not have PAMs. PAM recognition is also required for catalytic activity. Plasmids containing sequences homologous to endogenous spacer elements and that have flanking PAM consensus sequences cannot transform this strain unless the cas9 gene is disrupted or critical residues of Cas9 are mutated.<ref>PMID:23706818</ref> <ref>PMID:23940360</ref>	+	[https://www.uniprot.org/uniprot/CAS9_NEIM8 CAS9_NEIM8] 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). In type II CRISPR systems correct processing of pre-crRNA requires a trans-encoded small RNA (tracrRNA), endogenous ribonuclease 3 (rnc) and this protein, although RNase 3 is not required for 5'-processing of crRNA in this strain. Cas9/crRNA/tracrRNA endonucleolytically cleaves linear or circular dsDNA target complementary to the spacer; Cas9 is inactive in the absence of the 2 guide RNAs (gRNA, PubMed:23940360). Cas9 recognizes the protospacer adjacent motif (PAM) in the CRISPR repeat sequences to help distinguish self versus nonself, as targets within the bacterial CRISPR locus do not have PAMs. PAM recognition is also required for catalytic activity. Plasmids containing sequences homologous to endogenous spacer elements and that have flanking PAM consensus sequences cannot transform this strain unless the cas9 gene is disrupted or critical residues of Cas9 are mutated.<ref>PMID:23706818</ref> <ref>PMID:23940360</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 6je9" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6je9" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Endonuclease 3D structures\|Endonuclease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Neim8~~]]	+	[[Category: Neisseria meningitidis 8013]]
-	[[Category: Cheng, Z]]	+	[[Category: Synthetic construct]]
-	[[Category: Huang, X]]	+	[[Category: Cheng Z]]
-	[[Category: Liu, C]]	+	[[Category: Huang X]]
-	[[Category: Sun, W]]	+	[[Category: Liu C]]
-	[[Category: Wang, K]]	+	[[Category: Sun W]]
-	[[Category: Wang, Y]]	+	[[Category: Wang K]]
-	[[Category: Yang, J]]	+	[[Category: Wang Y]]
-	~~[[Category: Acriic3]]~~	+	[[Category: Yang J]]
-	~~[[Category: Anti-crispr]]~~	+
-	~~[[Category: Crispr-cas9]]~~	+
-	~~[[Category: Dimer]]~~	+
-	~~[[Category: Hydrolase]]~~	+
-	~~[[Category: Hydrolase-hydrolase inhibitor-rna complex]]~~	+
-	~~[[Category: Nme1cas9]]~~	+
-	~~[[Category: Nmecas9~~]]	+

OCA at 11:34, 13 November 2019

OCA — Wed, 13 Nov 2019 11:34:58 GMT

←Older revision		Revision as of 11:34, 13 November 2019
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	<StructureSection load='6je9' size='340' side='right'caption='[[6je9]], [[Resolution\|resolution]] 3.46Å' scene=''>		<StructureSection load='6je9' size='340' side='right'caption='[[6je9]], [[Resolution\|resolution]] 3.46Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6je9]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JE9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6JE9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6je9]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Neim8 Neim8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JE9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6JE9 FirstGlance]. <br>
-	</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=6je9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6je9 OCA], [http://pdbe.org/6je9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6je9 RCSB], [http://www.ebi.ac.uk/pdbsum/6je9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6je9 ProSAT]</span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cas9, NMV_1993 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=604162 NEIM8])</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=6je9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6je9 OCA], [http://pdbe.org/6je9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6je9 RCSB], [http://www.ebi.ac.uk/pdbsum/6je9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6je9 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/CAS9_NEIM8 CAS9_NEIM8]] 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). In type II CRISPR systems correct processing of pre-crRNA requires a trans-encoded small RNA (tracrRNA), endogenous ribonuclease 3 (rnc) and this protein, although RNase 3 is not required for 5'-processing of crRNA in this strain. Cas9/crRNA/tracrRNA endonucleolytically cleaves linear or circular dsDNA target complementary to the spacer; Cas9 is inactive in the absence of the 2 guide RNAs (gRNA, PubMed:23940360). Cas9 recognizes the protospacer adjacent motif (PAM) in the CRISPR repeat sequences to help distinguish self versus nonself, as targets within the bacterial CRISPR locus do not have PAMs. PAM recognition is also required for catalytic activity. Plasmids containing sequences homologous to endogenous spacer elements and that have flanking PAM consensus sequences cannot transform this strain unless the cas9 gene is disrupted or critical residues of Cas9 are mutated.<ref>PMID:23706818</ref> <ref>PMID:23940360</ref>		[[http://www.uniprot.org/uniprot/CAS9_NEIM8 CAS9_NEIM8]] 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). In type II CRISPR systems correct processing of pre-crRNA requires a trans-encoded small RNA (tracrRNA), endogenous ribonuclease 3 (rnc) and this protein, although RNase 3 is not required for 5'-processing of crRNA in this strain. Cas9/crRNA/tracrRNA endonucleolytically cleaves linear or circular dsDNA target complementary to the spacer; Cas9 is inactive in the absence of the 2 guide RNAs (gRNA, PubMed:23940360). Cas9 recognizes the protospacer adjacent motif (PAM) in the CRISPR repeat sequences to help distinguish self versus nonself, as targets within the bacterial CRISPR locus do not have PAMs. PAM recognition is also required for catalytic activity. Plasmids containing sequences homologous to endogenous spacer elements and that have flanking PAM consensus sequences cannot transform this strain unless the cas9 gene is disrupted or critical residues of Cas9 are mutated.<ref>PMID:23706818</ref> <ref>PMID:23940360</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	High-resolution Cas9 structures have yet to reveal catalytic conformations due to HNH nuclease domain positioning away from the cleavage site. Nme1Cas9 and Nme2Cas9 are compact nucleases for in vivo genome editing. Here, we report structures of meningococcal Cas9 homologs in complex with sgRNA, dsDNA, or the AcrIIC3 anti-CRISPR protein. DNA-bound structures represent an early step of target recognition, a later HNH pre-catalytic state, the HNH catalytic state, and a cleaved-target-DNA-bound state. In the HNH catalytic state of Nme1Cas9, the active site is seen poised at the scissile phosphodiester linkage of the target strand, providing a high-resolution view of the active conformation. The HNH active conformation activates the RuvC domain. Our structures explain how Nme1Cas9 and Nme2Cas9 read distinct PAM sequences and how AcrIIC3 inhibits Nme1Cas9 activity. These structures provide insights into Cas9 domain rearrangements, guide-target engagement, cleavage mechanism, and anti-CRISPR inhibition, facilitating the optimization of these genome-editing platforms.
		+
		+	Structures of Neisseria meningitidis Cas9 Complexes in Catalytically Poised and Anti-CRISPR-Inhibited States.,Sun W, Yang J, Cheng Z, Amrani N, Liu C, Wang K, Ibraheim R, Edraki A, Huang X, Wang M, Wang J, Liu L, Sheng G, Yang Y, Lou J, Sontheimer EJ, Wang Y Mol Cell. 2019 Oct 22. pii: S1097-2765(19)30730-0. doi:, 10.1016/j.molcel.2019.09.025. PMID:31668930<ref>PMID:31668930</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6je9" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Neim8]]
	[[Category: Cheng, Z]]		[[Category: Cheng, Z]]
	[[Category: Huang, X]]		[[Category: Huang, X]]

OCA at 06:39, 6 November 2019

OCA — Wed, 06 Nov 2019 06:39:51 GMT

←Older revision		Revision as of 06:39, 6 November 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6je9 is ~~ON HOLD~~ ~~until Paper Publication~~	+	==Crystal structure of Nme1Cas9-sgRNA dimer mediated by double protein inhibitor AcrIIC3 monomers==
-		+	<StructureSection load='6je9' size='340' side='right'caption='[[6je9]], [[Resolution\|resolution]] 3.46Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6je9]] is a 6 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JE9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6JE9 FirstGlance]. <br>
-	~~Description~~:	+	</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=6je9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6je9 OCA], [http://pdbe.org/6je9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6je9 RCSB], [http://www.ebi.ac.uk/pdbsum/6je9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6je9 ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/CAS9_NEIM8 CAS9_NEIM8]] 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). In type II CRISPR systems correct processing of pre-crRNA requires a trans-encoded small RNA (tracrRNA), endogenous ribonuclease 3 (rnc) and this protein, although RNase 3 is not required for 5'-processing of crRNA in this strain. Cas9/crRNA/tracrRNA endonucleolytically cleaves linear or circular dsDNA target complementary to the spacer; Cas9 is inactive in the absence of the 2 guide RNAs (gRNA, PubMed:23940360). Cas9 recognizes the protospacer adjacent motif (PAM) in the CRISPR repeat sequences to help distinguish self versus nonself, as targets within the bacterial CRISPR locus do not have PAMs. PAM recognition is also required for catalytic activity. Plasmids containing sequences homologous to endogenous spacer elements and that have flanking PAM consensus sequences cannot transform this strain unless the cas9 gene is disrupted or critical residues of Cas9 are mutated.<ref>PMID:23706818</ref> <ref>PMID:23940360</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Cheng, Z]]
		+	[[Category: Huang, X]]
		+	[[Category: Liu, C]]
		+	[[Category: Sun, W]]
		+	[[Category: Wang, K]]
		+	[[Category: Wang, Y]]
		+	[[Category: Yang, J]]
		+	[[Category: Acriic3]]
		+	[[Category: Anti-crispr]]
		+	[[Category: Crispr-cas9]]
		+	[[Category: Dimer]]
		+	[[Category: Hydrolase]]
		+	[[Category: Hydrolase-hydrolase inhibitor-rna complex]]
		+	[[Category: Nme1cas9]]
		+	[[Category: Nmecas9]]

OCA at 13:33, 27 February 2019

OCA — Wed, 27 Feb 2019 13:33:17 GMT

←Older revision		Revision as of 13:33, 27 February 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6je9 is ON HOLD	+	The entry 6je9 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA at 04:58, 21 February 2019

OCA — Thu, 21 Feb 2019 04:58:19 GMT

←Older revision		Revision as of 04:58, 21 February 2019
Line 3:		Line 3:
	The entry 6je9 is ON HOLD		The entry 6je9 is ON HOLD

-	Authors: ~~Cheng, Z., Huang, X., Sun, W., Wang, Y.~~	+	Authors:

-	Description: ~~Crystal structure of Nme1Cas9-sgRNA dimer mediated by protein inhibitor AcrIIC3~~	+	Description:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Sun, W]]
-	[[Category: Wang, Y]]
-	[[Category: Huang, X]]
-	[[Category: Cheng, Z]]

OCA: Protected "6je9" [edit=sysop:move=sysop]

OCA — Wed, 13 Feb 2019 07:27:09 GMT

Protected "6je9" [edit=sysop:move=sysop]

←Older revision

Revision as of 07:27, 13 February 2019

OCA: New page: '''Unreleased structure''' The entry 6je9 is ON HOLD Authors: Cheng, Z., Huang, X., Sun, W., Wang, Y. Description: Crystal structure of Nme1Cas9-sgRNA dimer mediated by protein inhibit...

OCA — Wed, 13 Feb 2019 07:27:08 GMT

New page: '''Unreleased structure''' The entry 6je9 is ON HOLD Authors: Cheng, Z., Huang, X., Sun, W., Wang, Y. Description: Crystal structure of Nme1Cas9-sgRNA dimer mediated by protein inhibit...

New page

'''Unreleased structure'''

The entry 6je9 is ON HOLD

Authors: Cheng, Z., Huang, X., Sun, W., Wang, Y.

Description: Crystal structure of Nme1Cas9-sgRNA dimer mediated by protein inhibitor AcrIIC3
[[Category: Unreleased Structures]]
[[Category: Sun, W]]
[[Category: Wang, Y]]
[[Category: Huang, X]]
[[Category: Cheng, Z]]