5vvj - Revision history

OCA at 13:59, 4 October 2023

OCA — Wed, 04 Oct 2023 13:59:33 GMT

←Older revision		Revision as of 13:59, 4 October 2023
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	<StructureSection load='5vvj' size='340' side='right'caption='[[5vvj]], [[Resolution\|resolution]] 3.89Å' scene=''>		<StructureSection load='5vvj' size='340' side='right'caption='[[5vvj]], [[Resolution\|resolution]] 3.89Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5vvj]] is a 8 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Ecoli Ecoli~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VVJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5VVJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5vvj]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12] 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=5VVJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5VVJ FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~ygbT~~, ~~cas1, b2755, JW2725 (~~[~~http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI~~]~~), ygbF, cas2, b2754, JW5438 ([http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=83333 ECOLI])~~</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]] 3.89Å</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=5vvj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vvj OCA], [~~http~~://pdbe.org/5vvj PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5vvj RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5vvj PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5vvj 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=5vvj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vvj OCA], [https://pdbe.org/5vvj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5vvj RCSB], [https://www.ebi.ac.uk/pdbsum/5vvj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5vvj ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/CAS1_ECOLI CAS1_ECOLI]] 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 sequences complementary to antecedent mobile elements and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA). Cas1 is thought to be involved in CRISPR adaptation, the first stage of CRISPR immunity. Might be involved in the addition/removal of CRISPR spacers. Endonucleolytically cleaves linear ssRNA, ssDNA and short (34 base) dsDNA as well as branched DNA substrates such as Holliday junctions, replication forks and 5'-flap DNA substrates. Genetic interactions suggest Cas1 interacts with components of the RecBC and RuvB DNA repair systems.<ref>PMID:21255106</ref> [[http://www.uniprot.org/uniprot/CAS2_ECOLI CAS2_ECOLI]] 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 sequences complementary to antecedent mobile elements and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA). Functions as a ssRNA-specific endoribonuclease (By similarity).<ref>PMID:21255106</ref>	+	[https://www.uniprot.org/uniprot/CAS1_ECOLI CAS1_ECOLI] 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 sequences complementary to antecedent mobile elements and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA). Cas1 is thought to be involved in CRISPR adaptation, the first stage of CRISPR immunity. Might be involved in the addition/removal of CRISPR spacers. Endonucleolytically cleaves linear ssRNA, ssDNA and short (34 base) dsDNA as well as branched DNA substrates such as Holliday junctions, replication forks and 5'-flap DNA substrates. Genetic interactions suggest Cas1 interacts with components of the RecBC and RuvB DNA repair systems.<ref>PMID:21255106</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Ecoli~~]]	+	[[Category: Escherichia coli K-12]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Doudna, J A~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Doxzen, K W~~]]	+	[[Category: Doudna JA]]
-	[[Category: ~~Knott, G J~~]]	+	[[Category: Doxzen KW]]
-	[[Category: ~~Wright, A V~~]]	+	[[Category: Knott GJ]]
-	[[Category: ~~Complex]]~~	+	[[Category: Wright AV]]
-	~~[[Category: Dna]]~~	+
-	~~[[Category: Hydrolase-dna complex~~]]	+

OCA at 08:05, 27 November 2019

OCA — Wed, 27 Nov 2019 08:05:13 GMT

←Older revision		Revision as of 08:05, 27 November 2019
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	==Cas1-Cas2 bound to half-site intermediate==		==Cas1-Cas2 bound to half-site intermediate==
-	<StructureSection load='5vvj' size='340' side='right' caption='[[5vvj]], [[Resolution\|resolution]] 3.89Å' scene=''>	+	<StructureSection load='5vvj' size='340' side='right'caption='[[5vvj]], [[Resolution\|resolution]] 3.89Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5vvj]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VVJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VVJ FirstGlance]. <br>		<table><tr><td colspan='2'>[[5vvj]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VVJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VVJ FirstGlance]. <br>
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	</div>		</div>
	<div class="pdbe-citations 5vvj" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5vvj" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Endonuclease 3D structures\|Endonuclease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Ecoli]]		[[Category: Ecoli]]
		+	[[Category: Large Structures]]
	[[Category: Doudna, J A]]		[[Category: Doudna, J A]]
	[[Category: Doxzen, K W]]		[[Category: Doxzen, K W]]

OCA at 14:42, 6 November 2017

OCA — Mon, 06 Nov 2017 14:42:15 GMT

←Older revision		Revision as of 14:42, 6 November 2017
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	<StructureSection load='5vvj' size='340' side='right' caption='[[5vvj]], [[Resolution\|resolution]] 3.89Å' scene=''>		<StructureSection load='5vvj' size='340' side='right' caption='[[5vvj]], [[Resolution\|resolution]] 3.89Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5vvj]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VVJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VVJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5vvj]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VVJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VVJ 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=5vvj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vvj OCA], [http://pdbe.org/5vvj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vvj RCSB], [http://www.ebi.ac.uk/pdbsum/5vvj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vvj ProSAT]</span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">ygbT, cas1, b2755, JW2725 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI]), ygbF, cas2, b2754, JW5438 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=5vvj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vvj OCA], [http://pdbe.org/5vvj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vvj RCSB], [http://www.ebi.ac.uk/pdbsum/5vvj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vvj ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Ecoli]]
	[[Category: Doudna, J A]]		[[Category: Doudna, J A]]
	[[Category: Doxzen, K W]]		[[Category: Doxzen, K W]]

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

OCA — Fri, 04 Aug 2017 04:07:04 GMT

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

←Older revision

Revision as of 04:07, 4 August 2017

OCA: New page: ==Cas1-Cas2 bound to half-site intermediate== == Structural highl...

OCA — Fri, 04 Aug 2017 04:07:02 GMT

New page: ==Cas1-Cas2 bound to half-site intermediate== <StructureSection load='5vvj' size='340' side='right' caption='5vvj, resolution 3.89Å' scene=''> == Structural highl...

New page

==Cas1-Cas2 bound to half-site intermediate==
<StructureSection load='5vvj' size='340' side='right' caption='[[5vvj]], [[Resolution|resolution]] 3.89Å' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5vvj]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VVJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VVJ 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=5vvj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vvj OCA], [http://pdbe.org/5vvj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vvj RCSB], [http://www.ebi.ac.uk/pdbsum/5vvj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vvj ProSAT]</span></td></tr>
</table>
== Function ==
[[http://www.uniprot.org/uniprot/CAS1_ECOLI CAS1_ECOLI]] 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 sequences complementary to antecedent mobile elements and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA). Cas1 is thought to be involved in CRISPR adaptation, the first stage of CRISPR immunity. Might be involved in the addition/removal of CRISPR spacers. Endonucleolytically cleaves linear ssRNA, ssDNA and short (34 base) dsDNA as well as branched DNA substrates such as Holliday junctions, replication forks and 5'-flap DNA substrates. Genetic interactions suggest Cas1 interacts with components of the RecBC and RuvB DNA repair systems.<ref>PMID:21255106</ref> [[http://www.uniprot.org/uniprot/CAS2_ECOLI CAS2_ECOLI]] 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 sequences complementary to antecedent mobile elements and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA). Functions as a ssRNA-specific endoribonuclease (By similarity).<ref>PMID:21255106</ref>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
CRISPR-Cas systems depend on the Cas1-Cas2 integrase to capture and integrate short foreign DNA fragments into the CRISPR locus, enabling adaptation to new viruses. We present crystal structures of Cas1-Cas2 bound to both donor and target DNA in intermediate and product integration complexes, as well as a cryo-electron microscopy structure of the full CRISPR locus integration complex including the accessory protein Integration Host Factor (IHF). The structures show unexpectedly that indirect sequence recognition dictates integration site selection by favoring deformation of the repeat and the flanking sequences. IHF binding bends the DNA sharply, bringing an upstream recognition motif into contact with Cas1 to increase both the specificity and efficiency of integration. These results explain how the Cas1-Cas2 CRISPR integrase recognizes a sequence-dependent DNA structure to ensure site-selective CRISPR array expansion during the initial step of bacterial adaptive immunity.

Structures of the CRISPR genome integration complex.,Wright AV, Liu JJ, Knott GJ, Doxzen KW, Nogales E, Doudna JA Science. 2017 Jul 20. pii: eaao0679. doi: 10.1126/science.aao0679. PMID:28729350<ref>PMID:28729350</ref>

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5vvj" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Doudna, J A]]
[[Category: Doxzen, K W]]
[[Category: Knott, G J]]
[[Category: Wright, A V]]
[[Category: Complex]]
[[Category: Dna]]
[[Category: Hydrolase-dna complex]]