3w2v - Revision history

OCA at 12:47, 8 November 2023

2023-11-08T12:47:38Z

←Older revision		Revision as of 12:47, 8 November 2023
Line 3:		Line 3:
	<StructureSection load='3w2v' size='340' side='right'caption='[[3w2v]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='3w2v' size='340' side='right'caption='[[3w2v]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3w2v]] is a 2 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=3W2V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3W2V FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3w2v]] is a 2 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=3W2V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3W2V FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3AM:[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-4-HYDROXY-2-(HYDROXYMETHYL)OXOLAN-3-YL]+DIHYDROGEN+PHOSPHATE'>3AM</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]] 2.6Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3w2w\|3w2w]]</div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3AM:[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-4-HYDROXY-2-(HYDROXYMETHYL)OXOLAN-3-YL]+DIHYDROGEN+PHOSPHATE'>3AM</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">cmr2, PF1129 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=186497 PYRFU]), cmr3, PF1128 ([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=3w2v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w2v OCA], [https://pdbe.org/3w2v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3w2v RCSB], [https://www.ebi.ac.uk/pdbsum/3w2v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3w2v 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=3w2v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w2v OCA], [https://pdbe.org/3w2v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3w2v RCSB], [https://www.ebi.ac.uk/pdbsum/3w2v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3w2v 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/CMR3_PYRFU CMR3_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.	+	[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 28:		Line 27:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Pyrfu~~]]	+	[[Category: Pyrococcus furiosus DSM 3638]]
-	[[Category: Numata, T]]	+	[[Category: Numata T]]
-	[[Category: Osawa, T]]	+	[[Category: Osawa T]]
-	~~[[Category: Ferredoxin-like fold]]~~	+
-	~~[[Category: Immune system~~]]	+

OCA at 05:20, 3 August 2022

2022-08-03T05:20:25Z

←Older revision		Revision as of 05:20, 3 August 2022
Line 1:		Line 1:

	==Crystal structure of the Cmr2dHD-Cmr3 subcomplex bound to 3'-AMP==		==Crystal structure of the Cmr2dHD-Cmr3 subcomplex bound to 3'-AMP==
-	<StructureSection load='3w2v' size='340' side='right' caption='[[3w2v]], [[Resolution\|resolution]] 2.60Å' scene=''>	+	<StructureSection load='3w2v' size='340' side='right'caption='[[3w2v]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3w2v]] is a 2 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=3W2V OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3W2V FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3w2v]] is a 2 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=3W2V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3W2V FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3AM:[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-4-HYDROXY-2-(HYDROXYMETHYL)OXOLAN-3-YL]+DIHYDROGEN+PHOSPHATE'>3AM</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=3AM:[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-4-HYDROXY-2-(HYDROXYMETHYL)OXOLAN-3-YL]+DIHYDROGEN+PHOSPHATE'>3AM</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">[[3w2w\|3w2w]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3w2w\|3w2w]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cmr2, PF1129 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=186497 PYRFU]), cmr3, PF1128 ([~~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">cmr2, PF1129 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=186497 PYRFU]), cmr3, PF1128 ([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=3w2v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w2v OCA], [~~http~~://pdbe.org/3w2v PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3w2v RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3w2v PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3w2v 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=3w2v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w2v OCA], [https://pdbe.org/3w2v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3w2v RCSB], [https://www.ebi.ac.uk/pdbsum/3w2v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3w2v 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> [[~~http~~://www.uniprot.org/uniprot/CMR3_PYRFU CMR3_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.	+	[[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/CMR3_PYRFU CMR3_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.
	<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: Numata, T]]		[[Category: Numata, T]]

OCA at 05:05, 5 August 2016

2016-08-05T05:05:42Z

←Older revision		Revision as of 05:05, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of the Cmr2dHD-Cmr3 subcomplex bound to 3'-AMP==		==Crystal structure of the Cmr2dHD-Cmr3 subcomplex bound to 3'-AMP==
	<StructureSection load='3w2v' size='340' side='right' caption='[[3w2v]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='3w2v' size='340' side='right' caption='[[3w2v]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3w2v]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Bionectria_wenpingii Bionectria wenpingii] and [http://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=3W2V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3W2V FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3w2v]] is a 2 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=3W2V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3W2V FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3AM:[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-4-HYDROXY-2-(HYDROXYMETHYL)OXOLAN-3-YL]+DIHYDROGEN+PHOSPHATE'>3AM</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=3AM:[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-4-HYDROXY-2-(HYDROXYMETHYL)OXOLAN-3-YL]+DIHYDROGEN+PHOSPHATE'>3AM</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">[[3w2w\|3w2w]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3w2w\|3w2w]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cmr2, PF1129 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=~~466134 Bionectria wenpingii~~]), cmr3, PF1128 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=186497 ~~Pyrococcus furiosus DSM 3638~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cmr2, PF1129 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=186497 PYRFU]), cmr3, PF1128 ([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=3w2v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w2v OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3w2v RCSB], [http://www.ebi.ac.uk/pdbsum/3w2v 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=3w2v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w2v OCA], [http://pdbe.org/3w2v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3w2v RCSB], [http://www.ebi.ac.uk/pdbsum/3w2v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3w2v 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 3w2v" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 25:		Line 27:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bionectria wenpingii]]~~	+	[[Category: Pyrfu]]
-	~~[[Category: Pyrococcus furiosus dsm 3638~~]]	+
	[[Category: Numata, T]]		[[Category: Numata, T]]
	[[Category: Osawa, T]]		[[Category: Osawa, T]]
	[[Category: Ferredoxin-like fold]]		[[Category: Ferredoxin-like fold]]
	[[Category: Immune system]]		[[Category: Immune system]]

OCA at 15:59, 25 December 2014

2014-12-25T15:59:50Z

←Older revision		Revision as of 15:59, 25 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3w2v\| PDB=3w2v \| SCENE= }}~~	+	==Crystal structure of the Cmr2dHD-Cmr3 subcomplex bound to 3'-AMP==
-	===Crystal structure of the Cmr2dHD-Cmr3 subcomplex bound to 3'-AMP===	+	<StructureSection load='3w2v' size='340' side='right' caption='[[3w2v]], [[Resolution\|resolution]] 2.60Å' scene=''>
-	~~{{ABSTRACT_PUBMED_23583914}}~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[3w2v]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bionectria_wenpingii Bionectria wenpingii] and [http://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=3W2V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3W2V FirstGlance]. <br>
-	==Function==	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=3AM:[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-4-HYDROXY-2-(HYDROXYMETHYL)OXOLAN-3-YL]+DIHYDROGEN+PHOSPHATE'>3AM</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">[[3w2w\|3w2w]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cmr2, PF1129 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=466134 Bionectria wenpingii]), cmr3, PF1128 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=186497 Pyrococcus furiosus DSM 3638])</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=3w2v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3w2v OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3w2v RCSB], [http://www.ebi.ac.uk/pdbsum/3w2v PDBsum]</span></td></tr>
		+	</table>
		+	== 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> [[http://www.uniprot.org/uniprot/CMR3_PYRFU CMR3_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.		[[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> [[http://www.uniprot.org/uniprot/CMR3_PYRFU CMR3_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.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Clustered, regularly interspaced, short palindromic repeat (CRISPR) loci found in prokaryotes are transcribed to produce CRISPR RNAs (crRNAs) that, together with CRISPR-associated (Cas) proteins, target and degrade invading genetic materials. Cmr proteins (Cmr1-6) and crRNA form a sequence-specific RNA silencing effector complex. Here, we report the crystal structures of the Pyrococcus furiosus Cmr2-Cmr3 subcomplex bound with nucleotides (3'-AMP or ATP). The association of Cmr2 and Cmr3 forms an idiosyncratic crevasse, which binds the nucleotides. Cmr3 shares structural similarity with Cas6, which cleaves precursor crRNA for maturation, suggesting the divergent evolution of these proteins. Due to the structural resemblance, the properties of the RNA binding surface observed in Cas6 are well conserved in Cmr3, indicating the RNA binding ability of Cmr3. This surface of Cmr3 constitutes the crevasse observed in the Cmr2-Cmr3 complex. Our findings suggest that the Cmr2-Cmr3 complex uses the crevasse to bind crRNA and/or substrate RNA during the reaction.
		+
		+	Crystal Structure of the Cmr2-Cmr3 Subcomplex in the CRISPR-Cas RNA Silencing Effector Complex.,Osawa T, Inanaga H, Numata T J Mol Biol. 2013 Oct 23;425(20):3811-3823. doi: 10.1016/j.jmb.2013.03.042. Epub, 2013 Apr 10. PMID:23583914<ref>PMID:23583914</ref>

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[3w2v]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Bionectria_wenpingii Bionectria wenpingii] and [http://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=3W2V OCA].~~	+	</div>

-	==~~Reference~~==	+	==See Also==
-	~~<ref group~~=~~"xtra">PMID:023583914</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	*[[Endonuclease\|Endonuclease]]
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Bionectria wenpingii]]		[[Category: Bionectria wenpingii]]
	[[Category: Pyrococcus furiosus dsm 3638]]		[[Category: Pyrococcus furiosus dsm 3638]]
-	[[Category: Numata, T.]]	+	[[Category: Numata, T]]
-	[[Category: Osawa, T.]]	+	[[Category: Osawa, T]]
	[[Category: Ferredoxin-like fold]]		[[Category: Ferredoxin-like fold]]
	[[Category: Immune system]]		[[Category: Immune system]]

OCA at 07:58, 16 October 2013

2013-10-16T07:58:25Z

←Older revision		Revision as of 07:58, 16 October 2013
Line 1:		Line 1:
-	~~'''Unreleased~~ structure'''	+	{{STRUCTURE_3w2v\| PDB=3w2v \| SCENE= }}
		+	===Crystal structure of the Cmr2dHD-Cmr3 subcomplex bound to 3'-AMP===
		+	{{ABSTRACT_PUBMED_23583914}}

-	~~The entry 3w2v~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	==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> [[http://www.uniprot.org/uniprot/CMR3_PYRFU CMR3_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.

-	~~Authors~~: ~~Numata, T~~.~~, Osawa, T~~.	+	==About this Structure==
		+	[[3w2v]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bionectria_wenpingii Bionectria wenpingii] and [http://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=3W2V OCA].

-	~~Description~~:	+	==Reference==
		+	<ref group="xtra">PMID:023583914</ref><references group="xtra"/><references/>
		+	[[Category: Bionectria wenpingii]]
		+	[[Category: Pyrococcus furiosus dsm 3638]]
		+	[[Category: Numata, T.]]
		+	[[Category: Osawa, T.]]
		+	[[Category: Ferredoxin-like fold]]
		+	[[Category: Immune system]]

OCA at 10:55, 23 January 2013

2013-01-23T10:55:55Z

←Older revision		Revision as of 10:55, 23 January 2013
Line 5:		Line 5:
	Authors: Numata, T., Osawa, T.		Authors: Numata, T., Osawa, T.

-	Description: ~~Crystal structure of the Cmr2dHD-Cmr3 subcomplex bound to 3'-AMP~~	+	Description:

OCA at 08:10, 16 January 2013

2013-01-16T08:10:01Z

←Older revision		Revision as of 08:10, 16 January 2013
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3w2v is ON HOLD	+	The entry 3w2v is ON HOLD until Paper Publication

	Authors: Numata, T., Osawa, T.		Authors: Numata, T., Osawa, T.

-	Description: ~~Cas proteins from Pyrococcus furiosus~~	+	Description: Crystal structure of the Cmr2dHD-Cmr3 subcomplex bound to 3'-AMP

OCA at 10:47, 19 December 2012

2012-12-19T10:47:50Z

←Older revision		Revision as of 10:47, 19 December 2012
Line 3:		Line 3:
	The entry 3w2v is ON HOLD		The entry 3w2v is ON HOLD

-	Authors: Numata,T., Osawa, T.	+	Authors: Numata, T., Osawa, T.

	Description: Cas proteins from Pyrococcus furiosus		Description: Cas proteins from Pyrococcus furiosus

OCA: Protected "3w2v" [edit=sysop:move=sysop]

2012-12-12T20:34:19Z

Protected "3w2v" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:34, 12 December 2012

OCA: New page: '''Unreleased structure''' The entry 3w2v is ON HOLD Authors: Numata,T., Osawa, T. Description: Cas proteins from Pyrococcus furiosus

2012-12-12T20:34:18Z

New page: '''Unreleased structure''' The entry 3w2v is ON HOLD Authors: Numata,T., Osawa, T. Description: Cas proteins from Pyrococcus furiosus

New page

'''Unreleased structure'''

The entry 3w2v is ON HOLD

Authors: Numata,T., Osawa, T.

Description: Cas proteins from Pyrococcus furiosus