3ur3 - Revision history

OCA at 10:29, 1 March 2024

2024-03-01T10:29:01Z

←Older revision		Revision as of 10:29, 1 March 2024
Line 3:		Line 3:
	<StructureSection load='3ur3' size='340' side='right'caption='[[3ur3]], [[Resolution\|resolution]] 2.41Å' scene=''>		<StructureSection load='3ur3' size='340' side='right'caption='[[3ur3]], [[Resolution\|resolution]] 2.41Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ur3]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Pyrfu Pyrfu~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UR3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3UR3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ur3]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus_DSM_3638 Pyrococcus furiosus DSM 3638]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UR3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3UR3 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>~~, ~~<scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>~~</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]] 2.405Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[3ung\|3ung]]~~</~~div~~><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">PF1129 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=186497 PYRFU])~~</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=3ur3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ur3 OCA], [https://pdbe.org/3ur3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ur3 RCSB], [https://www.ebi.ac.uk/pdbsum/3ur3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ur3 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=3ur3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ur3 OCA], [https://pdbe.org/3ur3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ur3 RCSB], [https://www.ebi.ac.uk/pdbsum/3ur3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ur3 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/CMR2_PYRFU CMR2_PYRFU]] 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), formerly called psiRNA (prokaryotic silencing) in this organism. Part of the Cmr ribonucleoprotein complex which has divalent cation-dependent endoribonuclease activity specific for ssRNA complementary to the crRNA, generating 5' hydroxy- and 3' phosphate or 2'-3' cyclic phosphate termini. It is not known which subunit has endoribonuclease activity. Cmr complex does not cleave ssDNA complementary to the crRNA. Cleavage of invading RNA is guided by the crRNA; substrate cleavage occurs a fixed distance (14 nt) from the 3' end of the crRNA. In vitro reconstitution shows Cmr1-2 and Cmr5 are not necessary for cleavage. Probably not the subunit that cleaves pre-crRNA, as mutation of numerous metal-binding residues have no effect on cleavage by assembled complex.<ref>PMID:19945378</ref>	+	[https://www.uniprot.org/uniprot/CMR2_PYRFU CMR2_PYRFU] 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), formerly called psiRNA (prokaryotic silencing) in this organism. Part of the Cmr ribonucleoprotein complex which has divalent cation-dependent endoribonuclease activity specific for ssRNA complementary to the crRNA, generating 5' hydroxy- and 3' phosphate or 2'-3' cyclic phosphate termini. It is not known which subunit has endoribonuclease activity. Cmr complex does not cleave ssDNA complementary to the crRNA. Cleavage of invading RNA is guided by the crRNA; substrate cleavage occurs a fixed distance (14 nt) from the 3' end of the crRNA. In vitro reconstitution shows Cmr1-2 and Cmr5 are not necessary for cleavage. Probably not the subunit that cleaves pre-crRNA, as mutation of numerous metal-binding residues have no effect on cleavage by assembled complex.<ref>PMID:19945378</ref>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Cmr2 is the largest and an essential subunit of a CRISPR RNA-Cas protein complex (the Cmr complex) that cleaves foreign RNA to protect prokaryotes from invading genetic elements. Cmr2 is thought to be the catalytic subunit of the effector complex because of its N-terminal HD nuclease domain. Here, however, we report that the HD domain of Cmr2 is not required for cleavage by the complex in vitro. The 2.3A crystal structure of Pyrococcus furiosus Cmr2 (lacking the HD domain) reveals two adenylyl cyclase-like and two alpha-helical domains. The adenylyl cyclase-like domains are arranged as in homodimeric adenylyl cyclases and bind ADP and divalent metals. However, mutagenesis studies show that the metal- and ADP-coordinating residues of Cmr2 are also not critical for cleavage by the complex. Our findings suggest that another component provides the catalytic function and that the essential role by Cmr2 does not require the identified ADP- or metal-binding or HD domains in vitro.	+
-		+
-	Structure of the Cmr2 Subunit of the CRISPR-Cas RNA Silencing Complex.,Cocozaki AI, Ramia NF, Shao Y, Hale CR, Terns RM, Terns MP, Li H Structure. 2012 Mar 7;20(3):545-53. PMID:22405013<ref>PMID:22405013</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 3ur3" style="background-color:#fffaf0;"></div~~>	+

	==See Also==		==See Also==
Line 28:		Line 18:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Pyrfu~~]]	+	[[Category: Pyrococcus furiosus DSM 3638]]
-	[[Category: Cocozaki~~, A I~~]]	+	[[Category: Cocozaki AI]]
-	[[Category: Hale~~, C R~~]]	+	[[Category: Hale CR]]
-	[[Category: Li, H]]	+	[[Category: Li H]]
-	[[Category: Ramia~~, N F~~]]	+	[[Category: Ramia NF]]
-	[[Category: Shao, Y]]	+	[[Category: Shao Y]]
-	[[Category: Terns~~, M P~~]]	+	[[Category: Terns MP]]
-	[[Category: Terns~~, R M]]~~	+	[[Category: Terns RM]]
-	~~[[Category: Cmr complex]]~~	+
-	~~[[Category: Ferredoxin fold]]~~	+
-	~~[[Category: Nucleotide-binding]]~~	+
-	~~[[Category: Polymerase]]~~	+
-	~~[[Category: Unknown function~~]]	+

OCA at 07:59, 20 July 2022

2022-07-20T07:59:25Z

←Older revision		Revision as of 07:59, 20 July 2022
Line 1:		Line 1:

	==Structure of the Cmr2 subunit of the CRISPR RNA silencing complex==		==Structure of the Cmr2 subunit of the CRISPR RNA silencing complex==
-	<StructureSection load='3ur3' size='340' side='right' caption='[[3ur3]], [[Resolution\|resolution]] 2.41Å' scene=''>	+	<StructureSection load='3ur3' size='340' side='right'caption='[[3ur3]], [[Resolution\|resolution]] 2.41Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ur3]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Pyrfu Pyrfu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UR3 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3UR3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ur3]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrfu Pyrfu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UR3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3UR3 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ung\|3ung]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3ung\|3ung]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PF1129 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=186497 PYRFU])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PF1129 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=186497 PYRFU])</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=3ur3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ur3 OCA], [~~http~~://pdbe.org/3ur3 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3ur3 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3ur3 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3ur3 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=3ur3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ur3 OCA], [https://pdbe.org/3ur3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ur3 RCSB], [https://www.ebi.ac.uk/pdbsum/3ur3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ur3 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/CMR2_PYRFU CMR2_PYRFU]] 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), formerly called psiRNA (prokaryotic silencing) in this organism. Part of the Cmr ribonucleoprotein complex which has divalent cation-dependent endoribonuclease activity specific for ssRNA complementary to the crRNA, generating 5' hydroxy- and 3' phosphate or 2'-3' cyclic phosphate termini. It is not known which subunit has endoribonuclease activity. Cmr complex does not cleave ssDNA complementary to the crRNA. Cleavage of invading RNA is guided by the crRNA; substrate cleavage occurs a fixed distance (14 nt) from the 3' end of the crRNA. In vitro reconstitution shows Cmr1-2 and Cmr5 are not necessary for cleavage. Probably not the subunit that cleaves pre-crRNA, as mutation of numerous metal-binding residues have no effect on cleavage by assembled complex.<ref>PMID:19945378</ref>	+	[[https://www.uniprot.org/uniprot/CMR2_PYRFU CMR2_PYRFU]] 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), formerly called psiRNA (prokaryotic silencing) in this organism. Part of the Cmr ribonucleoprotein complex which has divalent cation-dependent endoribonuclease activity specific for ssRNA complementary to the crRNA, generating 5' hydroxy- and 3' phosphate or 2'-3' cyclic phosphate termini. It is not known which subunit has endoribonuclease activity. Cmr complex does not cleave ssDNA complementary to the crRNA. Cleavage of invading RNA is guided by the crRNA; substrate cleavage occurs a fixed distance (14 nt) from the 3' end of the crRNA. In vitro reconstitution shows Cmr1-2 and Cmr5 are not necessary for cleavage. Probably not the subunit that cleaves pre-crRNA, as mutation of numerous metal-binding residues have no effect on cleavage by assembled complex.<ref>PMID:19945378</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 22:

	==See Also==		==See Also==
-	*[[Endonuclease\|Endonuclease]]	+	*[[Endonuclease 3D structures\|Endonuclease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Pyrfu]]		[[Category: Pyrfu]]
	[[Category: Cocozaki, A I]]		[[Category: Cocozaki, A I]]

OCA at 19:28, 11 August 2016

2016-08-11T19:28:37Z

←Older revision		Revision as of 19:28, 11 August 2016
Line 1:		Line 1:
		+
	==Structure of the Cmr2 subunit of the CRISPR RNA silencing complex==		==Structure of the Cmr2 subunit of the CRISPR RNA silencing complex==
	<StructureSection load='3ur3' size='340' side='right' caption='[[3ur3]], [[Resolution\|resolution]] 2.41Å' scene=''>		<StructureSection load='3ur3' size='340' side='right' caption='[[3ur3]], [[Resolution\|resolution]] 2.41Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ung\|3ung]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ung\|3ung]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PF1129 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=186497 PYRFU])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PF1129 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=186497 PYRFU])</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=3ur3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ur3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ur3 RCSB], [http://www.ebi.ac.uk/pdbsum/3ur3 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=3ur3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ur3 OCA], [http://pdbe.org/3ur3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ur3 RCSB], [http://www.ebi.ac.uk/pdbsum/3ur3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ur3 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 18:		Line 19:
	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 3ur3" style="background-color:#fffaf0;"></div>

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

OCA at 10:33, 7 February 2015

2015-02-07T10:33:30Z

←Older revision		Revision as of 10:33, 7 February 2015
Line 2:		Line 2:
	<StructureSection load='3ur3' size='340' side='right' caption='[[3ur3]], [[Resolution\|resolution]] 2.41Å' scene=''>		<StructureSection load='3ur3' size='340' side='right' caption='[[3ur3]], [[Resolution\|resolution]] 2.41Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3ur3]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Pyrococcus_furiosus Pyrococcus furiosus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UR3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3UR3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3ur3]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrfu Pyrfu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UR3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3UR3 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ung\|3ung]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ung\|3ung]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PF1129 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=~~2261 Pyrococcus furiosus~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PF1129 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=186497 PYRFU])</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=3ur3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ur3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ur3 RCSB], [http://www.ebi.ac.uk/pdbsum/3ur3 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=3ur3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ur3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ur3 RCSB], [http://www.ebi.ac.uk/pdbsum/3ur3 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[http://www.uniprot.org/uniprot/~~Q8U1S6_PYRFU Q8U1S6_PYRFU~~]] 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), formerly called psiRNA (prokaryotic silencing) in this organism. Part of the Cmr ribonucleoprotein complex which has divalent cation-dependent endoribonuclease activity specific for ssRNA complementary to the crRNA, generating 5' hydroxy- and 3' phosphate or 2'-3' cyclic phosphate termini. It is not known which subunit has endoribonuclease activity. Cmr complex does not cleave ssDNA complementary to the crRNA. Cleavage of invading RNA is guided by the crRNA; substrate cleavage occurs a fixed distance (14 nt) from the 3' end of the crRNA. In vitro reconstitution shows Cmr1-2 and Cmr5 are not necessary for cleavage. Probably not the subunit that cleaves pre-crRNA, as mutation of numerous metal-binding residues have no effect on cleavage by assembled complex.<ref>PMID:19945378</ref>	+	[[http://www.uniprot.org/uniprot/CMR2_PYRFU CMR2_PYRFU]] 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), formerly called psiRNA (prokaryotic silencing) in this organism. Part of the Cmr ribonucleoprotein complex which has divalent cation-dependent endoribonuclease activity specific for ssRNA complementary to the crRNA, generating 5' hydroxy- and 3' phosphate or 2'-3' cyclic phosphate termini. It is not known which subunit has endoribonuclease activity. Cmr complex does not cleave ssDNA complementary to the crRNA. Cleavage of invading RNA is guided by the crRNA; substrate cleavage occurs a fixed distance (14 nt) from the 3' end of the crRNA. In vitro reconstitution shows Cmr1-2 and Cmr5 are not necessary for cleavage. Probably not the subunit that cleaves pre-crRNA, as mutation of numerous metal-binding residues have no effect on cleavage by assembled complex.<ref>PMID:19945378</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 25:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Pyrococcus furiosus~~]]	+	[[Category: Pyrfu]]
	[[Category: Cocozaki, A I]]		[[Category: Cocozaki, A I]]
	[[Category: Hale, C R]]		[[Category: Hale, C R]]

OCA at 05:47, 25 December 2014

2014-12-25T05:47:53Z

←Older revision		Revision as of 05:47, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3ur3]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UR3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3UR3 FirstGlance]. <br>		<table><tr><td colspan='2'>[[3ur3]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UR3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3UR3 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ung\|3ung]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ung\|3ung]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PF1129 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2261 Pyrococcus furiosus])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PF1129 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2261 Pyrococcus furiosus])</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ur3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ur3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ur3 RCSB], [http://www.ebi.ac.uk/pdbsum/3ur3 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=3ur3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ur3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ur3 RCSB], [http://www.ebi.ac.uk/pdbsum/3ur3 PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/Q8U1S6_PYRFU Q8U1S6_PYRFU]] 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), formerly called psiRNA (prokaryotic silencing) in this organism. Part of the Cmr ribonucleoprotein complex which has divalent cation-dependent endoribonuclease activity specific for ssRNA complementary to the crRNA, generating 5' hydroxy- and 3' phosphate or 2'-3' cyclic phosphate termini. It is not known which subunit has endoribonuclease activity. Cmr complex does not cleave ssDNA complementary to the crRNA. Cleavage of invading RNA is guided by the crRNA; substrate cleavage occurs a fixed distance (14 nt) from the 3' end of the crRNA. In vitro reconstitution shows Cmr1-2 and Cmr5 are not necessary for cleavage. Probably not the subunit that cleaves pre-crRNA, as mutation of numerous metal-binding residues have no effect on cleavage by assembled complex.<ref>PMID:19945378</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 14:		Line 16:
	Structure of the Cmr2 Subunit of the CRISPR-Cas RNA Silencing Complex.,Cocozaki AI, Ramia NF, Shao Y, Hale CR, Terns RM, Terns MP, Li H Structure. 2012 Mar 7;20(3):545-53. PMID:22405013<ref>PMID:22405013</ref>		Structure of the Cmr2 Subunit of the CRISPR-Cas RNA Silencing Complex.,Cocozaki AI, Ramia NF, Shao Y, Hale CR, Terns RM, Terns MP, Li H Structure. 2012 Mar 7;20(3):545-53. PMID:22405013<ref>PMID:22405013</ref>

-	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, 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/>
Line 21:		Line 26:
	</StructureSection>		</StructureSection>
	[[Category: Pyrococcus furiosus]]		[[Category: Pyrococcus furiosus]]
-	[[Category: Cocozaki, A I.]]	+	[[Category: Cocozaki, A I]]
-	[[Category: Hale, C R.]]	+	[[Category: Hale, C R]]
-	[[Category: Li, H.]]	+	[[Category: Li, H]]
-	[[Category: Ramia, N F.]]	+	[[Category: Ramia, N F]]
-	[[Category: Shao, Y.]]	+	[[Category: Shao, Y]]
-	[[Category: Terns, M P.]]	+	[[Category: Terns, M P]]
-	[[Category: Terns, R M.]]	+	[[Category: Terns, R M]]
	[[Category: Cmr complex]]		[[Category: Cmr complex]]
	[[Category: Ferredoxin fold]]		[[Category: Ferredoxin fold]]

OCA at 06:44, 5 June 2014

2014-06-05T06:44:28Z

←Older revision		Revision as of 06:44, 5 June 2014
Line 1:		Line 1:
-	[[~~Image:~~3ur3.~~jpg~~\|~~left~~\|~~200px~~]]	+	==Structure of the Cmr2 subunit of the CRISPR RNA silencing complex==
		+	<StructureSection load='3ur3' size='340' side='right' caption='[[3ur3]], [[Resolution\|resolution]] 2.41Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3ur3]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UR3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3UR3 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ung\|3ung]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PF1129 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2261 Pyrococcus furiosus])</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ur3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ur3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ur3 RCSB], [http://www.ebi.ac.uk/pdbsum/3ur3 PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Cmr2 is the largest and an essential subunit of a CRISPR RNA-Cas protein complex (the Cmr complex) that cleaves foreign RNA to protect prokaryotes from invading genetic elements. Cmr2 is thought to be the catalytic subunit of the effector complex because of its N-terminal HD nuclease domain. Here, however, we report that the HD domain of Cmr2 is not required for cleavage by the complex in vitro. The 2.3A crystal structure of Pyrococcus furiosus Cmr2 (lacking the HD domain) reveals two adenylyl cyclase-like and two alpha-helical domains. The adenylyl cyclase-like domains are arranged as in homodimeric adenylyl cyclases and bind ADP and divalent metals. However, mutagenesis studies show that the metal- and ADP-coordinating residues of Cmr2 are also not critical for cleavage by the complex. Our findings suggest that another component provides the catalytic function and that the essential role by Cmr2 does not require the identified ADP- or metal-binding or HD domains in vitro.

-	<!--	+	Structure of the Cmr2 Subunit of the CRISPR-Cas RNA Silencing Complex.,Cocozaki AI, Ramia NF, Shao Y, Hale CR, Terns RM, Terns MP, Li H Structure. 2012 Mar 7;20(3):545-53. PMID:22405013<ref>PMID:22405013</ref>
-	~~The line below this paragraph~~, ~~containing "STRUCTURE_3ur3"~~, ~~creates the "~~Structure ~~Box" on the page~~.	+
-	~~You may change the PDB parameter~~ (~~which sets the PDB file loaded into the applet~~)	+
-	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded),~~	+
-	~~or leave the SCENE parameter empty for the default display~~.	+
-	-->	+
-	~~{{STRUCTURE_3ur3\| PDB=3ur3 \| SCENE= }}~~	+

-	~~===Structure~~ of the ~~Cmr2 subunit of the CRISPR RNA silencing complex===~~	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-		+	== References ==
-	~~<!--~~	+	<references/>
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_22405013}}, adds the Publication Abstract to the page~~	+	__TOC__
-	~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 22405013 is the PubMed ID number~~.	+	</StructureSection>
-	-->	+
-	~~{{ABSTRACT_PUBMED_22405013}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3ur3]] is a 1 chain structure with sequence from [http:~~/~~/en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UR3 OCA].~~	+
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:022405013<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Pyrococcus furiosus]]		[[Category: Pyrococcus furiosus]]
	[[Category: Cocozaki, A I.]]		[[Category: Cocozaki, A I.]]

OCA at 07:39, 21 March 2012

2012-03-21T07:39:26Z

←Older revision		Revision as of 07:39, 21 March 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3ur3.jpg\|left\|200px]]

-	The ~~entry 3ur3~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3ur3", creates the "Structure Box" on the page.
		+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
		+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
		+	or leave the SCENE parameter empty for the default display.
		+	-->
		+	{{STRUCTURE_3ur3\| PDB=3ur3 \| SCENE= }}

-	~~Authors: Cocozaki, A.I., Ramia, N.F., Shao, Y., Hale, C.R., Terns, R.M., Terns, M.P., Li, H.~~	+	===Structure of the Cmr2 subunit of the CRISPR RNA silencing complex===

-	~~Description: Structure of~~ the ~~Cmr2 subunit of~~ the ~~CRISPR RNA silencing~~ complex	+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_22405013}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 22405013 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_22405013}}
		+
		+	==About this Structure==
		+	[[3ur3]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UR3 OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:022405013</ref><references group="xtra"/>
		+	[[Category: Pyrococcus furiosus]]
		+	[[Category: Cocozaki, A I.]]
		+	[[Category: Hale, C R.]]
		+	[[Category: Li, H.]]
		+	[[Category: Ramia, N F.]]
		+	[[Category: Shao, Y.]]
		+	[[Category: Terns, M P.]]
		+	[[Category: Terns, R M.]]
		+	[[Category: Cmr complex]]
		+	[[Category: Ferredoxin fold]]
		+	[[Category: Nucleotide-binding]]
		+	[[Category: Polymerase]]
		+	[[Category: Unknown function]]

OCA at 06:49, 1 February 2012

2012-02-01T06:49:14Z

←Older revision		Revision as of 06:49, 1 February 2012
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3ur3 is ON HOLD	+	The entry 3ur3 is ON HOLD until Paper Publication

	Authors: Cocozaki, A.I., Ramia, N.F., Shao, Y., Hale, C.R., Terns, R.M., Terns, M.P., Li, H.		Authors: Cocozaki, A.I., Ramia, N.F., Shao, Y., Hale, C.R., Terns, R.M., Terns, M.P., Li, H.

	Description: Structure of the Cmr2 subunit of the CRISPR RNA silencing complex		Description: Structure of the Cmr2 subunit of the CRISPR RNA silencing complex

OCA: Protected "3ur3" [edit=sysop:move=sysop]

2011-11-30T05:55:19Z

Protected "3ur3" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:55, 30 November 2011

OCA: New page: '''Unreleased structure''' The entry 3ur3 is ON HOLD Authors: Cocozaki, A.I., Ramia, N.F., Shao, Y., Hale, C.R., Terns, R.M., Terns, M.P., Li, H. Description: Structure of the Cmr2 sub...

2011-11-30T05:55:18Z

New page: '''Unreleased structure''' The entry 3ur3 is ON HOLD Authors: Cocozaki, A.I., Ramia, N.F., Shao, Y., Hale, C.R., Terns, R.M., Terns, M.P., Li, H. Description: Structure of the Cmr2 sub...

New page

'''Unreleased structure'''

The entry 3ur3 is ON HOLD

Authors: Cocozaki, A.I., Ramia, N.F., Shao, Y., Hale, C.R., Terns, R.M., Terns, M.P., Li, H.

Description: Structure of the Cmr2 subunit of the CRISPR RNA silencing complex