5ds6 - Revision history

OCA at 21:57, 28 June 2023

2023-06-28T21:57:23Z

←Older revision		Revision as of 21:57, 28 June 2023
Line 3:		Line 3:
	<StructureSection load='5ds6' size='340' side='right'caption='[[5ds6]], [[Resolution\|resolution]] 3.35Å' scene=''>		<StructureSection load='5ds6' size='340' side='right'caption='[[5ds6]], [[Resolution\|resolution]] 3.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ds6]] 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=5DS6 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5DS6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ds6]] 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/Escherichia_virus_M13 Escherichia virus M13]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DS6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5DS6 FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[4p6i\|4p6i]]</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]] 3.352Å</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'>[https://proteopedia.org/fgij/fg.htm?mol=5ds6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ds6 OCA], [https://pdbe.org/5ds6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ds6 RCSB], [https://www.ebi.ac.uk/pdbsum/5ds6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ds6 ProSAT]</span></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=5ds6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ds6 OCA], [~~http~~://pdbe.org/5ds6 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5ds6 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5ds6 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5ds6 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: Escherichia virus M13]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Doudna~~, J A~~]]	+	[[Category: Doudna JA]]
-	[[Category: Engelman~~, A N~~]]	+	[[Category: Engelman AN]]
-	[[Category: Harrington~~, L B~~]]	+	[[Category: Harrington LB]]
-	[[Category: Kranzusch~~, P J~~]]	+	[[Category: Kranzusch PJ]]
-	[[Category: Nunez~~, J K]]~~	+	[[Category: Nunez JK]]
-	~~[[Category: Adaptive immunity]]~~	+
-	~~[[Category: Clustered regularly interspaced short palindromic repeat]]~~	+
-	~~[[Category: Crispr-associated protein]]~~	+
-	~~[[Category: Crispr-cas system]]~~	+
-	~~[[Category: Dna binding protein]]~~	+
-	~~[[Category: Endodeoxyribonuclease]]~~	+
-	~~[[Category: Endonuclease]]~~	+
-	~~[[Category: Hydrolase-dna complex]]~~	+
-	~~[[Category: Integrase~~]]	+

OCA at 16:08, 20 November 2019

2019-11-20T16:08:52Z

←Older revision		Revision as of 16:08, 20 November 2019
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	==Crystal structure the Escherichia coli Cas1-Cas2 complex bound to protospacer DNA with splayed ends==		==Crystal structure the Escherichia coli Cas1-Cas2 complex bound to protospacer DNA with splayed ends==
-	<StructureSection load='5ds6' size='340' side='right' caption='[[5ds6]], [[Resolution\|resolution]] 3.35Å' scene=''>	+	<StructureSection load='5ds6' size='340' side='right'caption='[[5ds6]], [[Resolution\|resolution]] 3.35Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5ds6]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DS6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DS6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5ds6]] 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=5DS6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DS6 FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4p6i\|4p6i]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4p6i\|4p6i]]</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=5ds6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ds6 OCA], [http://pdbe.org/5ds6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ds6 RCSB], [http://www.ebi.ac.uk/pdbsum/5ds6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ds6 ProSAT]</span></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=5ds6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ds6 OCA], [http://pdbe.org/5ds6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ds6 RCSB], [http://www.ebi.ac.uk/pdbsum/5ds6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ds6 ProSAT]</span></td></tr>
	</table>		</table>
Line 18:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5ds6" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5ds6" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Endonuclease 3D structures\|Endonuclease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Ecoli]]
		+	[[Category: Large Structures]]
	[[Category: Doudna, J A]]		[[Category: Doudna, J A]]
	[[Category: Engelman, A N]]		[[Category: Engelman, A N]]

OCA at 14:51, 16 November 2017

2017-11-16T14:51:19Z

←Older revision		Revision as of 14:51, 16 November 2017
Line 18:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 5ds6" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5ds6" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Endonuclease\|Endonuclease]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 16:56, 18 August 2017

2017-08-18T16:56:50Z

←Older revision		Revision as of 16:56, 18 August 2017
Line 5:		Line 5:
	<table><tr><td colspan='2'>[[5ds6]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DS6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DS6 FirstGlance]. <br>		<table><tr><td colspan='2'>[[5ds6]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DS6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DS6 FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4p6i\|4p6i]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4p6i\|4p6i]]</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=5ds6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ds6 OCA], [http://pdbe.org/5ds6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ds6 RCSB], [http://www.ebi.ac.uk/pdbsum/5ds6 PDBsum]</span></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=5ds6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ds6 OCA], [http://pdbe.org/5ds6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ds6 RCSB], [http://www.ebi.ac.uk/pdbsum/5ds6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ds6 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 5ds6" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5ds6" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Endonuclease\|Endonuclease]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 16:29, 10 May 2016

2016-05-10T16:29:22Z

←Older revision		Revision as of 16:29, 10 May 2016
Line 1:		Line 1:
		+
	==Crystal structure the Escherichia coli Cas1-Cas2 complex bound to protospacer DNA with splayed ends==		==Crystal structure the Escherichia coli Cas1-Cas2 complex bound to protospacer DNA with splayed ends==
	<StructureSection load='5ds6' size='340' side='right' caption='[[5ds6]], [[Resolution\|resolution]] 3.35Å' scene=''>		<StructureSection load='5ds6' size='340' side='right' caption='[[5ds6]], [[Resolution\|resolution]] 3.35Å' scene=''>

OCA at 19:42, 30 November 2015

2015-11-30T19:42:24Z

←Older revision		Revision as of 19:42, 30 November 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Crystal structure the Escherichia coli Cas1-Cas2 complex bound to protospacer DNA with splayed ends==
		+	<StructureSection load='5ds6' size='340' side='right' caption='[[5ds6]], [[Resolution\|resolution]] 3.35Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5ds6]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5DS6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5DS6 FirstGlance]. <br>
		+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4p6i\|4p6i]]</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=5ds6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ds6 OCA], [http://pdbe.org/5ds6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ds6 RCSB], [http://www.ebi.ac.uk/pdbsum/5ds6 PDBsum]</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 ==
		+	Bacteria and archaea generate adaptive immunity against phages and plasmids by integrating foreign DNA of specific 30-40-base-pair lengths into clustered regularly interspaced short palindromic repeat (CRISPR) loci as spacer segments. The universally conserved Cas1-Cas2 integrase complex catalyses spacer acquisition using a direct nucleophilic integration mechanism similar to retroviral integrases and transposases. How the Cas1-Cas2 complex selects foreign DNA substrates for integration remains unknown. Here we present X-ray crystal structures of the Escherichia coli Cas1-Cas2 complex bound to cognate 33-nucleotide protospacer DNA substrates. The protein complex creates a curved binding surface spanning the length of the DNA and splays the ends of the protospacer to allow each terminal nucleophilic 3'-OH to enter a channel leading into the Cas1 active sites. Phosphodiester backbone interactions between the protospacer and the proteins explain the sequence-nonspecific substrate selection observed in vivo. Our results uncover the structural basis for foreign DNA capture and the mechanism by which Cas1-Cas2 functions as a molecular ruler to dictate the sequence architecture of CRISPR loci.

-	~~The entry 5ds6 is ON HOLD until Paper Publication~~	+	Foreign DNA capture during CRISPR-Cas adaptive immunity.,Nunez JK, Harrington LB, Kranzusch PJ, Engelman AN, Doudna JA Nature. 2015 Nov 26;527(7579):535-8. doi: 10.1038/nature15760. Epub 2015 Oct 21. PMID:26503043<ref>PMID:26503043</ref>

-	~~Authors: Nunez~~, J.K., Harrington, L.B., Kranzusch, P.J~~., Engelman, A.N., Doudna~~, J~~.A.~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~:	+	<div class="pdbe-citations 5ds6" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Unreleased Structures~~]]	+	== References ==
-	[[Category: ~~Kranzusch, P.J~~]]	+	<references/>
-	[[Category: ~~Harrington, L.B~~]]	+	__TOC__
-	[[Category: ~~Doudna, J.A~~]]	+	</StructureSection>
-	[[Category: ~~Engelman, A.N~~]]	+	[[Category: Doudna, J A]]
-	[[Category: ~~Nunez, J.K~~]]	+	[[Category: Engelman, A N]]
		+	[[Category: Harrington, L B]]
		+	[[Category: Kranzusch, P J]]
		+	[[Category: Nunez, J K]]
		+	[[Category: Adaptive immunity]]
		+	[[Category: Clustered regularly interspaced short palindromic repeat]]
		+	[[Category: Crispr-associated protein]]
		+	[[Category: Crispr-cas system]]
		+	[[Category: Dna binding protein]]
		+	[[Category: Endodeoxyribonuclease]]
		+	[[Category: Endonuclease]]
		+	[[Category: Hydrolase-dna complex]]
		+	[[Category: Integrase]]

OCA: Protected "5ds6" [edit=sysop:move=sysop]

2015-09-30T13:27:06Z

Protected "5ds6" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:27, 30 September 2015

OCA: New page: '''Unreleased structure''' The entry 5ds6 is ON HOLD until Paper Publication Authors: Nunez, J.K., Harrington, L.B., Kranzusch, P.J., Engelman, A.N., Doudna, J.A. Description: [[Categ...

2015-09-30T13:27:05Z

New page: '''Unreleased structure''' The entry 5ds6 is ON HOLD until Paper Publication Authors: Nunez, J.K., Harrington, L.B., Kranzusch, P.J., Engelman, A.N., Doudna, J.A. Description: [[Categ...

New page

'''Unreleased structure'''

The entry 5ds6 is ON HOLD until Paper Publication

Authors: Nunez, J.K., Harrington, L.B., Kranzusch, P.J., Engelman, A.N., Doudna, J.A.

Description:
[[Category: Unreleased Structures]]
[[Category: Kranzusch, P.J]]
[[Category: Harrington, L.B]]
[[Category: Doudna, J.A]]
[[Category: Engelman, A.N]]
[[Category: Nunez, J.K]]