4ilm - Revision history

OCA at 11:57, 1 March 2024

OCA — Fri, 01 Mar 2024 11:57:44 GMT

←Older revision		Revision as of 11:57, 1 March 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4ilm]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharolobus_solfataricus_P2 Saccharolobus solfataricus P2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ILM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ILM FirstGlance]. <br>		<table><tr><td colspan='2'>[[4ilm]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharolobus_solfataricus_P2 Saccharolobus solfataricus P2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ILM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ILM FirstGlance]. <br>
-	</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=4ilm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ilm OCA], [https://pdbe.org/4ilm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ilm RCSB], [https://www.ebi.ac.uk/pdbsum/4ilm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ilm ProSAT]</span></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]] 3.068Å</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=4ilm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ilm OCA], [https://pdbe.org/4ilm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ilm RCSB], [https://www.ebi.ac.uk/pdbsum/4ilm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ilm ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/CAS6B_SACS2 CAS6B_SACS2] 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, generating an 8 base-long tag known as the 5' handle.<ref>PMID:21507944</ref>		[https://www.uniprot.org/uniprot/CAS6B_SACS2 CAS6B_SACS2] 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, generating an 8 base-long tag known as the 5' handle.<ref>PMID:21507944</ref>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Clustered regularly interspaced short palindromic repeats (CRISPRs) confer adaptive immunity to prokaryotes through a small RNA-mediated mechanism. Specific endoribonucleases are required by all CRISPR-bearing organisms to process CRISPR RNAs into small RNA that serve as guides for defensive effector complexes. The molecular mechanism of how the endoribonucleases process the class of CRISPR RNA containing no predicted secondary structural features remains largely elusive. Here, we report cocrystal structures of a processing endoribonuclease bound with a noncleavable RNA substrate and its product-like fragment derived from a nonpalindramic repeat. The enzyme stabilizes a short RNA stem-loop structure near the cleavage site and cleaves the phosphodiester bond using an active site comprised of arginine and lysine residues. The distinct RNA binding and cleavage mechanisms underline the diversity in CRISPR RNA processing.
-
-	Recognition and Cleavage of a Nonstructured CRISPR RNA by Its Processing Endoribonuclease Cas6.,Shao Y, Li H Structure. 2013 Feb 27. pii: S0969-2126(13)00017-8. doi:, 10.1016/j.str.2013.01.010. PMID:23454186<ref>PMID:23454186</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4ilm" style="background-color:#fffaf0;"></div>

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

OCA at 20:54, 16 November 2022

OCA — Wed, 16 Nov 2022 20:54:21 GMT

←Older revision		Revision as of 20:54, 16 November 2022
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	==CRISPR RNA Processing endoribonuclease==		==CRISPR RNA Processing endoribonuclease==
-	<StructureSection load='4ilm' size='340' side='right' caption='[[4ilm]], [[Resolution\|resolution]] 3.07Å' scene=''>	+	<StructureSection load='4ilm' size='340' side='right'caption='[[4ilm]], [[Resolution\|resolution]] 3.07Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4ilm]] is a 16 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Sulso Sulso~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ILM OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4ILM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4ilm]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharolobus_solfataricus_P2 Saccharolobus solfataricus P2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ILM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4ILM FirstGlance]. <br>
-	</td></tr>~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3pkm\|3pkm]], [[4ill\|4ill]], [[4ilr\|4ilr]]</td></tr>~~	+	</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=4ilm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ilm OCA], [https://pdbe.org/4ilm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ilm RCSB], [https://www.ebi.ac.uk/pdbsum/4ilm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ilm ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cas6b, SSO2004 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=273057 SULSO])</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=4ilm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ilm OCA], [~~http~~://pdbe.org/4ilm PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4ilm RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4ilm PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4ilm ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/CAS6B_SACS2 CAS6B_SACS2] 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, generating an 8 base-long tag known as the 5' handle.<ref>PMID:21507944</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 19:		Line 19:

	==See Also==		==See Also==
-	*[[Endonuclease\|Endonuclease]]	+	*[[Endonuclease 3D structures\|Endonuclease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Sulso~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Li, H~~]]	+	[[Category: Saccharolobus solfataricus P2]]
-	[[Category: ~~Shao, Y~~]]	+	[[Category: Li H]]
-	[[Category: ~~Endoribonuclease]]~~	+	[[Category: Shao Y]]
-	~~[[Category: Hydrolase-rna complex]]~~	+
-	~~[[Category: Rna]]~~	+
-	~~[[Category: Rrm~~]]	+

OCA at 07:08, 5 August 2016

OCA — Fri, 05 Aug 2016 07:08:33 GMT

←Older revision		Revision as of 07:08, 5 August 2016
Line 1:		Line 1:
		+
	==CRISPR RNA Processing endoribonuclease==		==CRISPR RNA Processing endoribonuclease==
	<StructureSection load='4ilm' size='340' side='right' caption='[[4ilm]], [[Resolution\|resolution]] 3.07Å' scene=''>		<StructureSection load='4ilm' size='340' side='right' caption='[[4ilm]], [[Resolution\|resolution]] 3.07Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4ilm]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Sulfolobus_solfataricus_p2 Sulfolobus solfataricus p2~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ILM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ILM FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4ilm]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Sulso Sulso]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ILM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ILM FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3pkm\|3pkm]], [[4ill\|4ill]], [[4ilr\|4ilr]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3pkm\|3pkm]], [[4ill\|4ill]], [[4ilr\|4ilr]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cas6b, SSO2004 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=273057 ~~Sulfolobus solfataricus P2~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cas6b, SSO2004 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=273057 SULSO])</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=4ilm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ilm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ilm RCSB], [http://www.ebi.ac.uk/pdbsum/4ilm 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=4ilm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ilm OCA], [http://pdbe.org/4ilm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4ilm RCSB], [http://www.ebi.ac.uk/pdbsum/4ilm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4ilm ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 15:		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>
		+	<div class="pdbe-citations 4ilm" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Endonuclease\|Endonuclease]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Sulfolobus solfataricus p2~~]]	+	[[Category: Sulso]]
	[[Category: Li, H]]		[[Category: Li, H]]
	[[Category: Shao, Y]]		[[Category: Shao, Y]]

OCA at 12:33, 21 December 2014

OCA — Sun, 21 Dec 2014 12:33:58 GMT

←Older revision		Revision as of 12:33, 21 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4ilm~~\| ~~PDB~~=4ilm \| ~~SCENE~~= }}	+	==CRISPR RNA Processing endoribonuclease==
-	===~~CRISPR RNA Processing endoribonuclease~~===	+	<StructureSection load='4ilm' size='340' side='right' caption='[[4ilm]], [[Resolution\|resolution]] 3.07Å' scene=''>
-	~~{{ABSTRACT_PUBMED_23454186}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4ilm]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Sulfolobus_solfataricus_p2 Sulfolobus solfataricus p2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ILM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ILM FirstGlance]. <br>
		+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3pkm\|3pkm]], [[4ill\|4ill]], [[4ilr\|4ilr]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cas6b, SSO2004 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=273057 Sulfolobus solfataricus P2])</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=4ilm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ilm OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ilm RCSB], [http://www.ebi.ac.uk/pdbsum/4ilm PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Clustered regularly interspaced short palindromic repeats (CRISPRs) confer adaptive immunity to prokaryotes through a small RNA-mediated mechanism. Specific endoribonucleases are required by all CRISPR-bearing organisms to process CRISPR RNAs into small RNA that serve as guides for defensive effector complexes. The molecular mechanism of how the endoribonucleases process the class of CRISPR RNA containing no predicted secondary structural features remains largely elusive. Here, we report cocrystal structures of a processing endoribonuclease bound with a noncleavable RNA substrate and its product-like fragment derived from a nonpalindramic repeat. The enzyme stabilizes a short RNA stem-loop structure near the cleavage site and cleaves the phosphodiester bond using an active site comprised of arginine and lysine residues. The distinct RNA binding and cleavage mechanisms underline the diversity in CRISPR RNA processing.

-	~~==About this Structure==~~	+	Recognition and Cleavage of a Nonstructured CRISPR RNA by Its Processing Endoribonuclease Cas6.,Shao Y, Li H Structure. 2013 Feb 27. pii: S0969-2126(13)00017-8. doi:, 10.1016/j.str.2013.01.010. PMID:23454186<ref>PMID:23454186</ref>
-	~~[[4ilm]] is~~ a ~~16 chain structure with sequence from [http~~:~~//en~~.~~wikipedia~~.~~org~~/~~wiki/Sulfolobus_solfataricus_p2 Sulfolobus solfataricus p2]~~. ~~Full crystallographic information is available from [http~~://~~oca~~.~~weizmann~~.ac.il/~~oca-bin/ocashort?id~~=~~4ILM OCA].~~	+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Sulfolobus solfataricus p2]]		[[Category: Sulfolobus solfataricus p2]]
-	[[Category: Li, H.]]	+	[[Category: Li, H]]
-	[[Category: Shao, Y.]]	+	[[Category: Shao, Y]]
	[[Category: Endoribonuclease]]		[[Category: Endoribonuclease]]
	[[Category: Hydrolase-rna complex]]		[[Category: Hydrolase-rna complex]]
	[[Category: Rna]]		[[Category: Rna]]
	[[Category: Rrm]]		[[Category: Rrm]]

OCA at 06:42, 2 May 2013

OCA — Thu, 02 May 2013 06:42:33 GMT

←Older revision		Revision as of 06:42, 2 May 2013
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{STRUCTURE_4ilm\| PDB=4ilm \| SCENE= }}
		+	===CRISPR RNA Processing endoribonuclease===
		+	{{ABSTRACT_PUBMED_23454186}}

-	~~The entry~~ 4ilm is ~~ON HOLD~~	+	==About this Structure==
-		+	[[4ilm]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Sulfolobus_solfataricus_p2 Sulfolobus solfataricus p2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4ILM OCA].
-	~~Authors~~: ~~Shao, Y.,~~ Li, H.	+	[[Category: Sulfolobus solfataricus p2]]
-		+	[[Category: Li, H.]]
-	~~Description~~: ~~CRISPR RNA Processing endoribonuclease~~	+	[[Category: Shao, Y.]]
		+	[[Category: Endoribonuclease]]
		+	[[Category: Hydrolase-rna complex]]
		+	[[Category: Rna]]
		+	[[Category: Rrm]]

OCA at 11:11, 23 January 2013

OCA — Wed, 23 Jan 2013 11:11:10 GMT

←Older revision		Revision as of 11:11, 23 January 2013
Line 3:		Line 3:
	The entry 4ilm is ON HOLD		The entry 4ilm is ON HOLD

-	Authors: Shao, Y,, Li, H.	+	Authors: Shao, Y., Li, H.

	Description: CRISPR RNA Processing endoribonuclease		Description: CRISPR RNA Processing endoribonuclease

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

OCA — Wed, 09 Jan 2013 07:51:50 GMT

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

←Older revision

Revision as of 07:51, 9 January 2013

OCA: New page: '''Unreleased structure''' The entry 4ilm is ON HOLD Authors: Shao, Y,, Li, H. Description: CRISPR RNA Processing endoribonuclease

OCA — Wed, 09 Jan 2013 07:51:49 GMT

New page: '''Unreleased structure''' The entry 4ilm is ON HOLD Authors: Shao, Y,, Li, H. Description: CRISPR RNA Processing endoribonuclease

New page

'''Unreleased structure'''

The entry 4ilm is ON HOLD

Authors: Shao, Y,, Li, H.

Description: CRISPR RNA Processing endoribonuclease