5vgb - Revision history

OCA at 14:10, 13 March 2024

OCA — Wed, 13 Mar 2024 14:10:20 GMT

←Older revision		Revision as of 14:10, 13 March 2024
Line 3:		Line 3:
	<StructureSection load='5vgb' size='340' side='right'caption='[[5vgb]], [[Resolution\|resolution]] 1.50Å' scene=''>		<StructureSection load='5vgb' size='340' side='right'caption='[[5vgb]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5vgb]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VGB OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5VGB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5vgb]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Neisseria_meningitidis Neisseria meningitidis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VGB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5VGB FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.497Å</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=5vgb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vgb OCA], [~~http~~://pdbe.org/5vgb PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5vgb RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5vgb PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5vgb ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=5vgb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vgb OCA], [https://pdbe.org/5vgb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5vgb RCSB], [https://www.ebi.ac.uk/pdbsum/5vgb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5vgb ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/X5EPV9_NEIME X5EPV9_NEIME]] 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. 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; Cas9 is inactive in the absence of the 2 guide RNAs (gRNA). 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.[HAMAP-Rule:MF_01480]	+	[https://www.uniprot.org/uniprot/X5EPV9_NEIME X5EPV9_NEIME] 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. 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; Cas9 is inactive in the absence of the 2 guide RNAs (gRNA). 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.[HAMAP-Rule:MF_01480]
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	CRISPR-Cas9 proteins function within bacterial immune systems to target and destroy invasive DNA and have been harnessed as a robust technology for genome editing. Small bacteriophage-encoded anti-CRISPR proteins (Acrs) can inactivate Cas9, providing an efficient off switch for Cas9-based applications. Here, we show that two Acrs, AcrIIC1 and AcrIIC3, inhibit Cas9 by distinct strategies. AcrIIC1 is a broad-spectrum Cas9 inhibitor that prevents DNA cutting by multiple divergent Cas9 orthologs through direct binding to the conserved HNH catalytic domain of Cas9. A crystal structure of an AcrIIC1-Cas9 HNH domain complex shows how AcrIIC1 traps Cas9 in a DNA-bound but catalytically inactive state. By contrast, AcrIIC3 blocks activity of a single Cas9 ortholog and induces Cas9 dimerization while preventing binding to the target DNA. These two orthogonal mechanisms allow for separate control of Cas9 target binding and cleavage and suggest applications to allow DNA binding while preventing DNA cutting by Cas9.	+
-		+
-	A Broad-Spectrum Inhibitor of CRISPR-Cas9.,Harrington LB, Doxzen KW, Ma E, Liu JJ, Knott GJ, Edraki A, Garcia B, Amrani N, Chen JS, Cofsky JC, Kranzusch PJ, Sontheimer EJ, Davidson AR, Maxwell KL, Doudna JA Cell. 2017 Sep 7;170(6):1224-1233.e15. doi: 10.1016/j.cell.2017.07.037. Epub 2017, Aug 24. PMID:28844692<ref>PMID:28844692</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 5vgb" style="background-color:#fffaf0;"></div>~~	+

	==See Also==		==See Also==
	*[[Endonuclease 3D structures\|Endonuclease 3D structures]]		*[[Endonuclease 3D structures\|Endonuclease 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Doudna~~, J A~~]]	+	[[Category: Neisseria meningitidis]]
-	[[Category: Doxzen~~, K W~~]]	+	[[Category: Doudna JA]]
-	[[Category: Harrington~~, L B~~]]	+	[[Category: Doxzen KW]]
-	[[Category: Knott~~, G J~~]]	+	[[Category: Harrington LB]]
-	[[Category: Kranzusch~~, P J~~]]	+	[[Category: Knott GJ]]
-	[[Category: Ma, E]]	+	[[Category: Kranzusch PJ]]
-	~~[[Category: Hydrolase-hydrolase inhibitor complex]]~~	+	[[Category: Ma E]]
-	~~[[Category: Protein]]~~	+
-	~~[[Category: Rna~~]]	+

OCA at 08:36, 30 September 2020

OCA — Wed, 30 Sep 2020 08:36:29 GMT

←Older revision		Revision as of 08:36, 30 September 2020
Line 1:		Line 1:

	==Crystal structure of NmeCas9 HNH domain bound to anti-CRISPR AcrIIC1==		==Crystal structure of NmeCas9 HNH domain bound to anti-CRISPR AcrIIC1==
-	<StructureSection load='5vgb' size='340' side='right' caption='[[5vgb]], [[Resolution\|resolution]] 1.50Å' scene=''>	+	<StructureSection load='5vgb' size='340' side='right'caption='[[5vgb]], [[Resolution\|resolution]] 1.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5vgb]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VGB OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5VGB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5vgb]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VGB OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5VGB FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=5vgb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vgb OCA], [http://pdbe.org/5vgb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vgb RCSB], [http://www.ebi.ac.uk/pdbsum/5vgb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vgb 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=5vgb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vgb OCA], [http://pdbe.org/5vgb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vgb RCSB], [http://www.ebi.ac.uk/pdbsum/5vgb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vgb ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 5vgb" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5vgb" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Endonuclease 3D structures\|Endonuclease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Doudna, J A]]		[[Category: Doudna, J A]]
	[[Category: Doxzen, K W]]		[[Category: Doxzen, K W]]

OCA at 10:50, 13 September 2017

OCA — Wed, 13 Sep 2017 10:50:25 GMT

←Older revision		Revision as of 10:50, 13 September 2017
Line 9:		Line 9:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/X5EPV9_NEIME X5EPV9_NEIME]] 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. 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; Cas9 is inactive in the absence of the 2 guide RNAs (gRNA). 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.[HAMAP-Rule:MF_01480]		[[http://www.uniprot.org/uniprot/X5EPV9_NEIME X5EPV9_NEIME]] 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. 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; Cas9 is inactive in the absence of the 2 guide RNAs (gRNA). 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.[HAMAP-Rule:MF_01480]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	CRISPR-Cas9 proteins function within bacterial immune systems to target and destroy invasive DNA and have been harnessed as a robust technology for genome editing. Small bacteriophage-encoded anti-CRISPR proteins (Acrs) can inactivate Cas9, providing an efficient off switch for Cas9-based applications. Here, we show that two Acrs, AcrIIC1 and AcrIIC3, inhibit Cas9 by distinct strategies. AcrIIC1 is a broad-spectrum Cas9 inhibitor that prevents DNA cutting by multiple divergent Cas9 orthologs through direct binding to the conserved HNH catalytic domain of Cas9. A crystal structure of an AcrIIC1-Cas9 HNH domain complex shows how AcrIIC1 traps Cas9 in a DNA-bound but catalytically inactive state. By contrast, AcrIIC3 blocks activity of a single Cas9 ortholog and induces Cas9 dimerization while preventing binding to the target DNA. These two orthogonal mechanisms allow for separate control of Cas9 target binding and cleavage and suggest applications to allow DNA binding while preventing DNA cutting by Cas9.
		+
		+	A Broad-Spectrum Inhibitor of CRISPR-Cas9.,Harrington LB, Doxzen KW, Ma E, Liu JJ, Knott GJ, Edraki A, Garcia B, Amrani N, Chen JS, Cofsky JC, Kranzusch PJ, Sontheimer EJ, Davidson AR, Maxwell KL, Doudna JA Cell. 2017 Sep 7;170(6):1224-1233.e15. doi: 10.1016/j.cell.2017.07.037. Epub 2017, Aug 24. PMID:28844692<ref>PMID:28844692</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5vgb" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 14:52, 5 September 2017

OCA — Tue, 05 Sep 2017 14:52:57 GMT

←Older revision		Revision as of 14:52, 5 September 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5vgb is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of NmeCas9 HNH domain bound to anti-CRISPR AcrIIC1==
-		+	<StructureSection load='5vgb' size='340' side='right' caption='[[5vgb]], [[Resolution\|resolution]] 1.50Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5vgb]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VGB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VGB FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=5vgb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vgb OCA], [http://pdbe.org/5vgb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vgb RCSB], [http://www.ebi.ac.uk/pdbsum/5vgb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vgb ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/X5EPV9_NEIME X5EPV9_NEIME]] 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. 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; Cas9 is inactive in the absence of the 2 guide RNAs (gRNA). 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.[HAMAP-Rule:MF_01480]
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Doudna, J A]]
		+	[[Category: Doxzen, K W]]
		+	[[Category: Harrington, L B]]
		+	[[Category: Knott, G J]]
		+	[[Category: Kranzusch, P J]]
		+	[[Category: Ma, E]]
		+	[[Category: Hydrolase-hydrolase inhibitor complex]]
		+	[[Category: Protein]]
		+	[[Category: Rna]]

OCA at 12:15, 27 April 2017

OCA — Thu, 27 Apr 2017 12:15:51 GMT

←Older revision		Revision as of 12:15, 27 April 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5vgb is ON HOLD	+	The entry 5vgb is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "5vgb" [edit=sysop:move=sysop]

OCA — Wed, 19 Apr 2017 11:24:32 GMT

Protected "5vgb" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:24, 19 April 2017

OCA: New page: '''Unreleased structure''' The entry 5vgb is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 19 Apr 2017 11:24:30 GMT

New page: '''Unreleased structure''' The entry 5vgb is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5vgb is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]