6jdx - Revision history

OCA at 10:07, 22 November 2023

OCA — Wed, 22 Nov 2023 10:07:07 GMT

←Older revision		Revision as of 10:07, 22 November 2023
Line 3:		Line 3:
	<StructureSection load='6jdx' size='340' side='right'caption='[[6jdx]], [[Resolution\|resolution]] 2.28Å' scene=''>		<StructureSection load='6jdx' size='340' side='right'caption='[[6jdx]], [[Resolution\|resolution]] 2.28Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6jdx]] is a 3 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=6JDX OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6JDX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6jdx]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Neisseria_meningitidis_8013 Neisseria meningitidis 8013]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JDX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6JDX FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=EDO:1~~,2~~-ETHANEDIOL'>EDO</scene>~~</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]] 2.28Å</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='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></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=6jdx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jdx OCA], [~~http~~://pdbe.org/6jdx PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6jdx RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6jdx PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6jdx 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=6jdx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jdx OCA], [https://pdbe.org/6jdx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6jdx RCSB], [https://www.ebi.ac.uk/pdbsum/6jdx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6jdx 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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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Neim8~~]]	+	[[Category: Neisseria meningitidis 8013]]
-	[[Category: Cheng, Z]]	+	[[Category: Cheng Z]]
-	[[Category: Huang, X]]	+	[[Category: Huang X]]
-	[[Category: Sun, W]]	+	[[Category: Sun W]]
-	[[Category: Wang, Y]]	+	[[Category: Wang Y]]
-	~~[[Category: Acriic2]]~~	+
-	~~[[Category: Anti-crispr]]~~	+
-	~~[[Category: Crispr-cas9]]~~	+
-	~~[[Category: Hydrolase-hydrolase inhibitor complex]]~~	+
-	~~[[Category: Nme1cas9]]~~	+
-	~~[[Category: Nmecas9~~]]	+

OCA at 06:56, 31 July 2019

OCA — Wed, 31 Jul 2019 06:56:33 GMT

←Older revision		Revision as of 06:56, 31 July 2019
Line 10:		Line 10:
	== 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 ==
		+	CRISPR-Cas adaptive immune systems function to protect bacteria from invasion by foreign genetic elements. The CRISPR-Cas9 system has been widely adopted as a powerful genome-editing tool, and phage-encoded inhibitors, known as anti-CRISPRs, offer a means of regulating its activity. Here, we report the crystal structures of anti-CRISPR protein AcrIIC2Nme alone and in complex with Nme1Cas9. We demonstrate that AcrIIC2Nme inhibits Cas9 through interactions with the positively charged bridge helix, thereby preventing sgRNA loading. In vivo phage plaque assays and in vitro DNA cleavage assays show that AcrIIC2Nme mediates its activity through a large electronegative surface. This work shows that anti-CRISPR activity can be mediated through the inhibition of Cas9 complex assembly.
		+
		+	Inhibition of CRISPR-Cas9 ribonucleoprotein complex assembly by anti-CRISPR AcrIIC2.,Thavalingam A, Cheng Z, Garcia B, Huang X, Shah M, Sun W, Wang M, Harrington L, Hwang S, Hidalgo-Reyes Y, Sontheimer EJ, Doudna J, Davidson AR, Moraes TF, Wang Y, Maxwell KL Nat Commun. 2019 Jun 26;10(1):2806. doi: 10.1038/s41467-019-10577-3. PMID:31243272<ref>PMID:31243272</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6jdx" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Endonuclease 3D structures\|Endonuclease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:29, 21 May 2019

OCA — Tue, 21 May 2019 07:29:13 GMT

←Older revision		Revision as of 07:29, 21 May 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6jdx is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of AcrIIC2 dimer in complex with partial Nme1Cas9 preprocessed with protease alpha-Chymotrypsin==
-		+	<StructureSection load='6jdx' size='340' side='right'caption='[[6jdx]], [[Resolution\|resolution]] 2.28Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6jdx]] is a 3 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=6JDX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6JDX FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<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=6jdx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jdx OCA], [http://pdbe.org/6jdx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jdx RCSB], [http://www.ebi.ac.uk/pdbsum/6jdx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jdx ProSAT]</span></td></tr>
		+	</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: Neim8]]
		+	[[Category: Cheng, Z]]
		+	[[Category: Huang, X]]
		+	[[Category: Sun, W]]
		+	[[Category: Wang, Y]]
		+	[[Category: Acriic2]]
		+	[[Category: Anti-crispr]]
		+	[[Category: Crispr-cas9]]
		+	[[Category: Hydrolase-hydrolase inhibitor complex]]
		+	[[Category: Nme1cas9]]
		+	[[Category: Nmecas9]]

OCA at 13:33, 27 February 2019

OCA — Wed, 27 Feb 2019 13:33:02 GMT

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

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

	Authors:		Authors:

OCA at 04:58, 21 February 2019

OCA — Thu, 21 Feb 2019 04:58:10 GMT

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

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

-	Description: ~~Crystal structure of AcrIIC2 dimer in complex with partial Nme1Cas9~~	+	Description:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Sun, W]]
-	[[Category: Wang, Y]]
-	[[Category: Huang, X]]
-	[[Category: Cheng, Z]]

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

OCA — Wed, 13 Feb 2019 07:26:07 GMT

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

←Older revision

Revision as of 07:26, 13 February 2019

OCA: New page: '''Unreleased structure''' The entry 6jdx is ON HOLD Authors: Cheng, Z., Huang, X., Sun, W., Wang, Y. Description: Crystal structure of AcrIIC2 dimer in complex with partial Nme1Cas9 [...

OCA — Wed, 13 Feb 2019 07:26:05 GMT

New page: '''Unreleased structure''' The entry 6jdx is ON HOLD Authors: Cheng, Z., Huang, X., Sun, W., Wang, Y. Description: Crystal structure of AcrIIC2 dimer in complex with partial Nme1Cas9 [...

New page

'''Unreleased structure'''

The entry 6jdx is ON HOLD

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

Description: Crystal structure of AcrIIC2 dimer in complex with partial Nme1Cas9
[[Category: Unreleased Structures]]
[[Category: Sun, W]]
[[Category: Wang, Y]]
[[Category: Huang, X]]
[[Category: Cheng, Z]]