5y36 - Revision history

OCA at 10:21, 27 March 2024

2024-03-27T10:21:30Z

←Older revision		Revision as of 10:21, 27 March 2024
Line 3:		Line 3:
	<SX load='5y36' size='340' side='right' viewer='molstar' caption='[[5y36]], [[Resolution\|resolution]] 5.20Å' scene=''>		<SX load='5y36' size='340' side='right' viewer='molstar' caption='[[5y36]], [[Resolution\|resolution]] 5.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5y36]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y36 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5Y36 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5y36]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus] and [https://en.wikipedia.org/wiki/Streptococcus_pyogenes_serotype_M1 Streptococcus pyogenes serotype M1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y36 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5Y36 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 5.2Å</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=5y36 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y36 OCA], [~~http~~://pdbe.org/5y36 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5y36 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5y36 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5y36 ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=5y36 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y36 OCA], [https://pdbe.org/5y36 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5y36 RCSB], [https://www.ebi.ac.uk/pdbsum/5y36 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5y36 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://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 ==~~	+
-	CRISPR-Cas9 technology has been widely used for genome engineering. Its RNA-guided endonuclease Cas9 binds specifically to target DNA and then cleaves the two DNA strands with HNH and RuvC nuclease domains. However, structural information regarding the DNA cleavage-activating state of two nuclease domains remains sparse. Here, we report a 5.2 A cryo-EM structure of Cas9 in complex with sgRNA and target DNA. This structure reveals a conformational state of Cas9 in which the HNH domain is closest to the DNA cleavage site. Compared with two known HNH states, our structure shows that the HNH active site moves toward the cleavage site by about 25 and 13 A, respectively. In combination with EM-based molecular dynamics simulations, we show that residues of the nuclease domains in our structure could form cleavage-compatible conformations with the target DNA. Together, these results strongly suggest that our cryo-EM structure resembles a DNA cleavage-activating architecture of Cas9.	+
-		+
-	Structural insights into DNA cleavage activation of CRISPR-Cas9 system.,Huai C, Li G, Yao R, Zhang Y, Cao M, Kong L, Jia C, Yuan H, Chen H, Lu D, Huang Q Nat Commun. 2017 Nov 9;8(1):1375. doi: 10.1038/s41467-017-01496-2. PMID:29123204<ref>PMID:29123204</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 5y36" style="background-color:#fffaf0;"></div~~>	+

	==See Also==		==See Also==
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	</SX>		</SX>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Huai, C~~]]	+	[[Category: Mus musculus]]
-	[[Category: ~~Huang, Q~~]]	+	[[Category: Streptococcus pyogenes serotype M1]]
-	[[Category: ~~Li, G~~]]	+	[[Category: Huai C]]
-	[[Category: ~~Cripsr-cas9~~]]	+	[[Category: Huang Q]]
-	[[Category: ~~Dna cleavage mechanism]]~~	+	[[Category: Li G]]
-	~~[[Category: Genome editting]]~~	+
-	~~[[Category: Hydrolase-dna-rna complex]]~~	+
-	~~[[Category: Hydrolase-rna-dna complex~~]]	+

OCA at 22:40, 10 April 2020

2020-04-10T22:40:23Z

←Older revision		Revision as of 22:40, 10 April 2020
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	<SX load='5y36' size='340' side='right' viewer='molstar' caption='[[5y36]], [[Resolution\|resolution]] 5.20Å' scene=''>		<SX load='5y36' size='340' side='right' viewer='molstar' caption='[[5y36]], [[Resolution\|resolution]] 5.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5y36]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y36 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5Y36 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5y36]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y36 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5Y36 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=5y36 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y36 OCA], [http://pdbe.org/5y36 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y36 RCSB], [http://www.ebi.ac.uk/pdbsum/5y36 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y36 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=5y36 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y36 OCA], [http://pdbe.org/5y36 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y36 RCSB], [http://www.ebi.ac.uk/pdbsum/5y36 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y36 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 20:12, 6 March 2020

2020-03-06T20:12:40Z

←Older revision		Revision as of 20:12, 6 March 2020
Line 1:		Line 1:

	==Cryo-EM structure of SpCas9-sgRNA-DNA ternary complex==		==Cryo-EM structure of SpCas9-sgRNA-DNA ternary complex==
-	<~~StructureSection~~ load='5y36' size='340' side='right' caption='[[5y36]], [[Resolution\|resolution]] 5.20Å' scene=''>	+	<SX load='5y36' size='340' side='right' viewer='molstar' caption='[[5y36]], [[Resolution\|resolution]] 5.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5y36]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y36 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Y36 FirstGlance]. <br>		<table><tr><td colspan='2'>[[5y36]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y36 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Y36 FirstGlance]. <br>
Line 18:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 5y36" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5y36" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[CRISPR-Cas9\|CRISPR-Cas9]]
		+	*[[Endonuclease 3D structures\|Endonuclease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
-	</~~StructureSection~~>	+	</SX>
		+	[[Category: Large Structures]]
	[[Category: Huai, C]]		[[Category: Huai, C]]
	[[Category: Huang, Q]]		[[Category: Huang, Q]]

OCA at 07:21, 6 December 2017

2017-12-06T07:21:08Z

←Older revision		Revision as of 07:21, 6 December 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5y36 is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Cryo-EM structure of SpCas9-sgRNA-DNA ternary complex==
		+	<StructureSection load='5y36' size='340' side='right' caption='[[5y36]], [[Resolution\|resolution]] 5.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5y36]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Y36 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Y36 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=5y36 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5y36 OCA], [http://pdbe.org/5y36 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5y36 RCSB], [http://www.ebi.ac.uk/pdbsum/5y36 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5y36 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://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 ==
		+	CRISPR-Cas9 technology has been widely used for genome engineering. Its RNA-guided endonuclease Cas9 binds specifically to target DNA and then cleaves the two DNA strands with HNH and RuvC nuclease domains. However, structural information regarding the DNA cleavage-activating state of two nuclease domains remains sparse. Here, we report a 5.2 A cryo-EM structure of Cas9 in complex with sgRNA and target DNA. This structure reveals a conformational state of Cas9 in which the HNH domain is closest to the DNA cleavage site. Compared with two known HNH states, our structure shows that the HNH active site moves toward the cleavage site by about 25 and 13 A, respectively. In combination with EM-based molecular dynamics simulations, we show that residues of the nuclease domains in our structure could form cleavage-compatible conformations with the target DNA. Together, these results strongly suggest that our cryo-EM structure resembles a DNA cleavage-activating architecture of Cas9.

-	~~Authors~~:	+	Structural insights into DNA cleavage activation of CRISPR-Cas9 system.,Huai C, Li G, Yao R, Zhang Y, Cao M, Kong L, Jia C, Yuan H, Chen H, Lu D, Huang Q Nat Commun. 2017 Nov 9;8(1):1375. doi: 10.1038/s41467-017-01496-2. PMID:29123204<ref>PMID:29123204</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5y36" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Huai, C]]
		+	[[Category: Huang, Q]]
		+	[[Category: Li, G]]
		+	[[Category: Cripsr-cas9]]
		+	[[Category: Dna cleavage mechanism]]
		+	[[Category: Genome editting]]
		+	[[Category: Hydrolase-dna-rna complex]]
		+	[[Category: Hydrolase-rna-dna complex]]

OCA at 04:42, 1 November 2017

2017-11-01T04:42:34Z

←Older revision		Revision as of 04:42, 1 November 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5y36 is ON HOLD	+	The entry 5y36 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "5y36" [edit=sysop:move=sysop]

2017-09-27T16:04:59Z

Protected "5y36" [edit=sysop:move=sysop]

←Older revision

Revision as of 16:04, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5y36 is ON HOLD Authors: Description: Category: Unreleased Structures

2017-09-27T16:04:58Z

New page: '''Unreleased structure''' The entry 5y36 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5y36 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]