4w8v - Revision history

OCA at 11:27, 9 May 2024

OCA — Thu, 09 May 2024 11:27:13 GMT

←Older revision		Revision as of 11:27, 9 May 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4w8v]] 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=4W8V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4W8V FirstGlance]. <br>		<table><tr><td colspan='2'>[[4w8v]] 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=4W8V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4W8V 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=4w8v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4w8v OCA], [https://pdbe.org/4w8v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4w8v RCSB], [https://www.ebi.ac.uk/pdbsum/4w8v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4w8v 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]] 2.15Å</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=4w8v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4w8v OCA], [https://pdbe.org/4w8v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4w8v RCSB], [https://www.ebi.ac.uk/pdbsum/4w8v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4w8v ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 06:57, 7 April 2023

OCA — Fri, 07 Apr 2023 06:57:31 GMT

←Older revision		Revision as of 06:57, 7 April 2023
Line 3:		Line 3:
	<StructureSection load='4w8v' size='340' side='right'caption='[[4w8v]], [[Resolution\|resolution]] 2.15Å' scene=''>		<StructureSection load='4w8v' size='340' side='right'caption='[[4w8v]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4w8v]] 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=4W8V OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4W8V FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4w8v]] 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=4W8V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4W8V FirstGlance]. <br>
-	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cmr6, PF1124 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=186497 PYRFU])</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=4w8v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4w8v OCA], [https://pdbe.org/4w8v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4w8v RCSB], [https://www.ebi.ac.uk/pdbsum/4w8v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4w8v ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4w8v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4w8v OCA], [~~http~~://pdbe.org/4w8v PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4w8v RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4w8v PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4w8v ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/CMR6_PYRFU CMR6_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.<ref>PMID:19945378</ref>	+	[https://www.uniprot.org/uniprot/CMR6_PYRFU CMR6_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.<ref>PMID:19945378</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 22:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Pyrfu~~]]	+	[[Category: Pyrococcus furiosus DSM 3638]]
-	[[Category: Baumgaertner, M]]	+	[[Category: Baumgaertner M]]
-	[[Category: Benda, C]]	+	[[Category: Benda C]]
-	[[Category: Conti, E]]	+	[[Category: Conti E]]
-	[[Category: Ebert, J]]	+	[[Category: Ebert J]]
-	~~[[Category: Cmr complex]]~~	+
-	~~[[Category: Rna binding protein~~]]	+

OCA at 08:10, 23 May 2019

OCA — Thu, 23 May 2019 08:10:55 GMT

←Older revision		Revision as of 08:10, 23 May 2019
Line 1:		Line 1:

	==Crystal structure of Cmr6 from Pyrococcus furiosus==		==Crystal structure of Cmr6 from Pyrococcus furiosus==
-	<StructureSection load='4w8v' size='340' side='right' caption='[[4w8v]], [[Resolution\|resolution]] 2.15Å' scene=''>	+	<StructureSection load='4w8v' size='340' side='right'caption='[[4w8v]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4w8v]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4W8V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4W8V FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4w8v]] 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=4W8V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4W8V FirstGlance]. <br>
-	</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=4w8v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4w8v OCA], [http://pdbe.org/4w8v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4w8v RCSB], [http://www.ebi.ac.uk/pdbsum/4w8v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4w8v ProSAT]</span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cmr6, PF1124 ([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=4w8v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4w8v OCA], [http://pdbe.org/4w8v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4w8v RCSB], [http://www.ebi.ac.uk/pdbsum/4w8v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4w8v ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 21:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Pyrfu]]
	[[Category: Baumgaertner, M]]		[[Category: Baumgaertner, M]]
	[[Category: Benda, C]]		[[Category: Benda, C]]

OCA at 22:34, 5 August 2016

OCA — Fri, 05 Aug 2016 22:34:28 GMT

←Older revision		Revision as of 22:34, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of Cmr6 from Pyrococcus furiosus==		==Crystal structure of Cmr6 from Pyrococcus furiosus==
	<StructureSection load='4w8v' size='340' side='right' caption='[[4w8v]], [[Resolution\|resolution]] 2.15Å' scene=''>		<StructureSection load='4w8v' size='340' side='right' caption='[[4w8v]], [[Resolution\|resolution]] 2.15Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4w8v]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4W8V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4W8V FirstGlance]. <br>		<table><tr><td colspan='2'>[[4w8v]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4W8V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4W8V FirstGlance]. <br>
-	</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=4w8v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4w8v OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4w8v RCSB], [http://www.ebi.ac.uk/pdbsum/4w8v PDBsum]</span></td></tr>	+	</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=4w8v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4w8v OCA], [http://pdbe.org/4w8v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4w8v RCSB], [http://www.ebi.ac.uk/pdbsum/4w8v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4w8v ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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 4w8v" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 06:25, 25 December 2014

OCA — Thu, 25 Dec 2014 06:25:42 GMT

←Older revision		Revision as of 06:25, 25 December 2014
Line 5:		Line 5:
	</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=4w8v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4w8v OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4w8v RCSB], [http://www.ebi.ac.uk/pdbsum/4w8v PDBsum]</span></td></tr>		</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=4w8v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4w8v OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4w8v RCSB], [http://www.ebi.ac.uk/pdbsum/4w8v PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/CMR6_PYRFU CMR6_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.<ref>PMID:19945378</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 17:		Line 19:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Baumgaertner, M.]]	+	[[Category: Baumgaertner, M]]
-	[[Category: Benda, C.]]	+	[[Category: Benda, C]]
-	[[Category: Conti, E.]]	+	[[Category: Conti, E]]
-	[[Category: Ebert, J.]]	+	[[Category: Ebert, J]]
	[[Category: Cmr complex]]		[[Category: Cmr complex]]
	[[Category: Rna binding protein]]		[[Category: Rna binding protein]]

OCA at 10:36, 20 October 2014

OCA — Mon, 20 Oct 2014 10:36:45 GMT

←Older revision		Revision as of 10:36, 20 October 2014
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Crystal structure of Cmr6 from Pyrococcus furiosus==
		+	<StructureSection load='4w8v' size='340' side='right' caption='[[4w8v]], [[Resolution\|resolution]] 2.15Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4w8v]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4W8V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4W8V FirstGlance]. <br>
		+	</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=4w8v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4w8v OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4w8v RCSB], [http://www.ebi.ac.uk/pdbsum/4w8v PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The Cmr complex is an RNA-guided endonuclease that cleaves foreign RNA targets as part of the CRISPR prokaryotic defense system. We investigated the molecular architecture of the P. furiosus Cmr complex using an integrative structural biology approach. We determined crystal structures of P. furiosus Cmr1, Cmr2, Cmr4, and Cmr6 and combined them with known structural information to interpret the cryo-EM map of the complex. To support structure determination, we obtained residue-specific interaction data using protein crosslinking and mass spectrometry. The resulting pseudoatomic model reveals how the superhelical backbone of the complex is defined by the polymerizing principles of Cmr4 and Cmr5 and how it is capped at the extremities by proteins of similar folds. The inner surface of the superhelix exposes conserved residues of Cmr4 that we show are required for target-cleavage activity. The structural and biochemical data thus identify Cmr4 as the conserved endoribonuclease of the Cmr complex.

-	~~The entry 4w8v is ON HOLD until Paper Publication~~	+	Structural Model of a CRISPR RNA-Silencing Complex Reveals the RNA-Target Cleavage Activity in Cmr4.,Benda C, Ebert J, Scheltema RA, Schiller HB, Baumgartner M, Bonneau F, Mann M, Conti E Mol Cell. 2014 Oct 2;56(1):43-54. doi: 10.1016/j.molcel.2014.09.002. PMID:25280103<ref>PMID:25280103</ref>

-	~~Authors: Benda~~, C.~~, Ebert, J~~., Baumgaertner, M., Conti, E.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~:	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Baumgaertner, M.]]
		+	[[Category: Benda, C.]]
		+	[[Category: Conti, E.]]
		+	[[Category: Ebert, J.]]
		+	[[Category: Cmr complex]]
		+	[[Category: Rna binding protein]]

OCA at 09:04, 24 September 2014

OCA — Wed, 24 Sep 2014 09:04:04 GMT

←Older revision		Revision as of 09:04, 24 September 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4w8v is ON HOLD	+	The entry 4w8v is ON HOLD until Paper Publication

	Authors: Benda, C., Ebert, J., Baumgaertner, M., Conti, E.		Authors: Benda, C., Ebert, J., Baumgaertner, M., Conti, E.

	Description:		Description:

OCA: Protected "4w8v" [edit=sysop:move=sysop]

OCA — Thu, 04 Sep 2014 04:49:04 GMT

Protected "4w8v" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:49, 4 September 2014

OCA: New page: '''Unreleased structure''' The entry 4w8v is ON HOLD Authors: Benda, C., Ebert, J., Baumgaertner, M., Conti, E. Description:

OCA — Thu, 04 Sep 2014 04:49:02 GMT

New page: '''Unreleased structure''' The entry 4w8v is ON HOLD Authors: Benda, C., Ebert, J., Baumgaertner, M., Conti, E. Description:

New page

'''Unreleased structure'''

The entry 4w8v is ON HOLD

Authors: Benda, C., Ebert, J., Baumgaertner, M., Conti, E.

Description: