4n06 - Revision history

OCA at 10:22, 28 December 2022

OCA — Wed, 28 Dec 2022 10:22:56 GMT

←Older revision		Revision as of 10:22, 28 December 2022
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	<StructureSection load='4n06' size='340' side='right'caption='[[4n06]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='4n06' size='340' side='right'caption='[[4n06]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4n06]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Archaeoglobus_fulgidus~~ Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4N06 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4N06 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4n06]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Archaeoglobus_fulgidus_DSM_4304 Archaeoglobus fulgidus DSM 4304]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4N06 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4N06 FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=4n06 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4n06 OCA], [~~http~~://pdbe.org/4n06 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4n06 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4n06 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4n06 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=4n06 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4n06 OCA], [https://pdbe.org/4n06 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4n06 RCSB], [https://www.ebi.ac.uk/pdbsum/4n06 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4n06 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/CAS1A_ARCFU CAS1A_ARCFU]] 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). Acts as a dsDNA endonuclease. May be involved in the integration of spacer DNA into the CRISPR cassette (By similarity).	+	[https://www.uniprot.org/uniprot/CAS1A_ARCFU CAS1A_ARCFU] 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). Acts as a dsDNA endonuclease. May be involved in the integration of spacer DNA into the CRISPR cassette (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 20:

	==See Also==		==See Also==
-	*[[Endonuclease\|Endonuclease]]	+	*[[Endonuclease 3D structures\|Endonuclease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Archaeoglobus fulgidus]]	+	[[Category: Archaeoglobus fulgidus DSM 4304]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Kim~~, J S~~]]	+	[[Category: Kim JS]]
-	[[Category: Kim~~, T Y~~]]	+	[[Category: Kim TY]]
-	[[Category: Shin, M]]	+	[[Category: Shin M]]
-	[[Category: Yen~~, L H.T]]~~	+	[[Category: Yen LHT]]
-	~~[[Category: Hydrolase~~]]	+

OCA at 09:01, 10 April 2019

OCA — Wed, 10 Apr 2019 09:01:40 GMT

←Older revision		Revision as of 09:01, 10 April 2019
Line 1:		Line 1:

	==Crystal structure of Cas1 from Archaeoglobus fulgidus and its nucleolytic activity==		==Crystal structure of Cas1 from Archaeoglobus fulgidus and its nucleolytic activity==
-	<StructureSection load='4n06' size='340' side='right' caption='[[4n06]], [[Resolution\|resolution]] 2.40Å' scene=''>	+	<StructureSection load='4n06' size='340' side='right'caption='[[4n06]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4n06]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4N06 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4N06 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4n06]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4N06 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4N06 FirstGlance]. <br>
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	</StructureSection>		</StructureSection>
	[[Category: Archaeoglobus fulgidus]]		[[Category: Archaeoglobus fulgidus]]
		+	[[Category: Large Structures]]
	[[Category: Kim, J S]]		[[Category: Kim, J S]]
	[[Category: Kim, T Y]]		[[Category: Kim, T Y]]

OCA at 20:47, 5 August 2016

OCA — Fri, 05 Aug 2016 20:47:49 GMT

←Older revision		Revision as of 20:47, 5 August 2016
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		+
	==Crystal structure of Cas1 from Archaeoglobus fulgidus and its nucleolytic activity==		==Crystal structure of Cas1 from Archaeoglobus fulgidus and its nucleolytic activity==
	<StructureSection load='4n06' size='340' side='right' caption='[[4n06]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='4n06' size='340' side='right' caption='[[4n06]], [[Resolution\|resolution]] 2.40Å' scene=''>
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	<table><tr><td colspan='2'>[[4n06]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4N06 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4N06 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4n06]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4N06 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4N06 FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=4n06 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4n06 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4n06 RCSB], [http://www.ebi.ac.uk/pdbsum/4n06 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=4n06 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4n06 OCA], [http://pdbe.org/4n06 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4n06 RCSB], [http://www.ebi.ac.uk/pdbsum/4n06 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4n06 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 16:		Line 17:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4n06" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==

OCA at 05:45, 25 December 2014

OCA — Thu, 25 Dec 2014 05:45:35 GMT

←Older revision		Revision as of 05:45, 25 December 2014
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	<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=4n06 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4n06 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4n06 RCSB], [http://www.ebi.ac.uk/pdbsum/4n06 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=4n06 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4n06 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4n06 RCSB], [http://www.ebi.ac.uk/pdbsum/4n06 PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/CAS1A_ARCFU CAS1A_ARCFU]] 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). Acts as a dsDNA endonuclease. May be involved in the integration of spacer DNA into the CRISPR cassette (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 14:		Line 16:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+
		+	==See Also==
		+	*[[Endonuclease\|Endonuclease]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 18:50, 21 December 2014

OCA — Sun, 21 Dec 2014 18:50:18 GMT

←Older revision		Revision as of 18:50, 21 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4n06~~\| ~~PDB~~=4n06 \| ~~SCENE~~= }}	+	==Crystal structure of Cas1 from Archaeoglobus fulgidus and its nucleolytic activity==
-	===~~Crystal~~ structure of Cas1 from Archaeoglobus fulgidus and its ~~nucleolytic~~ activity~~===~~	+	<StructureSection load='4n06' size='340' side='right' caption='[[4n06]], [[Resolution\|resolution]] 2.40Å' scene=''>
-	~~{{ABSTRACT_PUBMED_24211577}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4n06]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4N06 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4N06 FirstGlance]. <br>
		+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=4n06 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4n06 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4n06 RCSB], [http://www.ebi.ac.uk/pdbsum/4n06 PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) and CRISPR-associated (Cas) proteins are involved in bacterial acquired immunity against incoming hazardous genetic materials. Cas1 is ubiquitous in CRISPR-containing microorganisms and supposed to recognize and cleave a foreign nucleic acid, and integrate the cleaved fragment into host genome using a yet unidentified mechanism. However, all the reported Cas1s did not show the nucleolytic activity, which makes its role still obscure. The elucidated crystal structure of Cas1 from Archaeoglobus fulgidus (AfCas1) shows a butterfly-like dimeric structure. The Asp out of three confirmed nucleolytic residues of Glu, His, and Asp in other Cas1s is replaced with Glu in AfCas1. Further, insertion of five residues into one of two loops, which are close to the catalytic center of and disordered in other Cas1 structures, partially covers the active site of AfCas1. Nonetheless, in vitro assays show that its nucleic acid-binding activity was not impaired against the tested single-stranded (ss) DNA, various forms of double-stranded (ds) DNA, or ssRNA with a hydrolyzing activity against ssRNA and dsDNA in a metal ion-dependent way. These results support the proposed Cas1's function at the early step of this bacterial immune system.

-	~~==Function==~~	+	Crystal structure of Cas1 from Archaeoglobus fulgidus and characterization of its nucleolytic activity.,Kim TY, Shin M, Huynh Thi Yen L, Kim JS Biochem Biophys Res Commun. 2013 Nov 29;441(4):720-5. doi:, 10.1016/j.bbrc.2013.10.122. Epub 2013 Nov 5. PMID:24211577<ref>PMID:24211577</ref>
-	~~[[http://www~~.~~uniprot~~.~~org/uniprot/CAS1A_ARCFU CAS1A_ARCFU]] 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)~~. ~~Acts as a dsDNA endonuclease~~. ~~May be involved in the integration of spacer DNA into the CRISPR cassette (By similarity)~~.	+

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[4n06]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=4N06 OCA].~~	+	</div>
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:024211577</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Archaeoglobus fulgidus]]		[[Category: Archaeoglobus fulgidus]]
-	[[Category: Kim, J S.]]	+	[[Category: Kim, J S]]
-	[[Category: Kim, T Y.]]	+	[[Category: Kim, T Y]]
-	[[Category: Shin, M.]]	+	[[Category: Shin, M]]
-	[[Category: Yen, L H.T.]]	+	[[Category: Yen, L H.T]]
	[[Category: Hydrolase]]		[[Category: Hydrolase]]

OCA at 08:12, 15 January 2014

OCA — Wed, 15 Jan 2014 08:12:17 GMT

←Older revision		Revision as of 08:12, 15 January 2014
Line 1:		Line 1:
-	~~'''Unreleased~~ structure~~'''~~	+	{{STRUCTURE_4n06\| PDB=4n06 \| SCENE= }}
		+	===Crystal structure of Cas1 from Archaeoglobus fulgidus and its nucleolytic activity===
		+	{{ABSTRACT_PUBMED_24211577}}

-	~~The entry 4n06~~ is ~~ON HOLD until Paper Publication~~	+	==Function==
		+	[[http://www.uniprot.org/uniprot/CAS1A_ARCFU CAS1A_ARCFU]] 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). Acts as a dsDNA endonuclease. May be involved in the integration of spacer DNA into the CRISPR cassette (By similarity).

-	~~Authors~~: ~~Kim, T~~.Y.~~, Shin, M~~.~~, Yen, L.H~~.T.~~, Kim, J~~.S.	+	==About this Structure==
		+	[[4n06]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Archaeoglobus_fulgidus Archaeoglobus fulgidus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4N06 OCA].

-	~~Description~~: ~~Crystal structure of Cas1 from~~ Archaeoglobus fulgidus ~~and its nucleolytic activity~~	+	==Reference==
		+	<ref group="xtra">PMID:024211577</ref><references group="xtra"/><references/>
		+	[[Category: Archaeoglobus fulgidus]]
		+	[[Category: Kim, J S.]]
		+	[[Category: Kim, T Y.]]
		+	[[Category: Shin, M.]]
		+	[[Category: Yen, L H.T.]]
		+	[[Category: Hydrolase]]

OCA: Protected "4n06" [edit=sysop:move=sysop]

OCA — Thu, 10 Oct 2013 05:52:29 GMT

Protected "4n06" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:52, 10 October 2013

OCA: New page: '''Unreleased structure''' The entry 4n06 is ON HOLD until Paper Publication Authors: Kim, T.Y., Shin, M., Yen, L.H.T., Kim, J.S. Description: Crystal structure of Cas1 from Archaeoglo...

OCA — Thu, 10 Oct 2013 05:52:28 GMT

New page: '''Unreleased structure''' The entry 4n06 is ON HOLD until Paper Publication Authors: Kim, T.Y., Shin, M., Yen, L.H.T., Kim, J.S. Description: Crystal structure of Cas1 from Archaeoglo...

New page

'''Unreleased structure'''

The entry 4n06 is ON HOLD until Paper Publication

Authors: Kim, T.Y., Shin, M., Yen, L.H.T., Kim, J.S.

Description: Crystal structure of Cas1 from Archaeoglobus fulgidus and its nucleolytic activity