3x1l - Revision history

OCA at 19:23, 29 May 2024

OCA — Wed, 29 May 2024 19:23:11 GMT

←Older revision		Revision as of 19:23, 29 May 2024
Line 1:		Line 1:

	==Crystal Structure of the CRISPR-Cas RNA Silencing Cmr Complex Bound to a Target Analog==		==Crystal Structure of the CRISPR-Cas RNA Silencing Cmr Complex Bound to a Target Analog==
-	<StructureSection load='3x1l' size='340' side='right'caption='[[3x1l]]' scene=''>	+	<StructureSection load='3x1l' size='340' side='right'caption='[[3x1l]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3X1L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3X1L FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3x1l]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Archaeoglobus_fulgidus_DSM_4304 Archaeoglobus fulgidus DSM 4304], [https://en.wikipedia.org/wiki/Pyrococcus_furiosus_COM1 Pyrococcus furiosus COM1], [https://en.wikipedia.org/wiki/Pyrococcus_furiosus_DSM_3638 Pyrococcus furiosus DSM 3638] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3X1L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3X1L 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=3x1l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3x1l OCA], [https://pdbe.org/3x1l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3x1l RCSB], [https://www.ebi.ac.uk/pdbsum/3x1l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3x1l 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]] 2.096Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=3x1l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3x1l OCA], [https://pdbe.org/3x1l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3x1l RCSB], [https://www.ebi.ac.uk/pdbsum/3x1l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3x1l ProSAT]</span></td></tr>
	</table>		</table>
		+	== 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>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	In prokaryotes, Clustered regularly interspaced short palindromic repeat (CRISPR)-derived RNAs (crRNAs), together with CRISPR-associated (Cas) proteins, capture and degrade invading genetic materials. In the type III-B CRISPR-Cas system, six Cas proteins (Cmr1-Cmr6) and a crRNA form an RNA silencing Cmr complex. Here we report the 2.1 A crystal structure of the Cmr1-deficient, functional Cmr complex bound to single-stranded DNA, a substrate analog complementary to the crRNA guide. Cmr3 recognizes the crRNA 5' tag and defines the start position of the guide-target duplex, using its idiosyncratic loops. The beta-hairpins of three Cmr4 subunits intercalate within the duplex, causing nucleotide displacements with 6 nt intervals, and thus periodically placing the scissile bonds near the crucial aspartate of Cmr4. The structure reveals the mechanism for specifying the periodic target cleavage sites from the crRNA 5' tag and provides insights into the assembly of the type III interference machineries and the evolution of the Cmr and Cascade complexes.
		+
		+	Crystal Structure of the CRISPR-Cas RNA Silencing Cmr Complex Bound to a Target Analog.,Osawa T, Inanaga H, Sato C, Numata T Mol Cell. 2015 May 7;58(3):418-30. doi: 10.1016/j.molcel.2015.03.018. Epub 2015, Apr 23. PMID:25921071<ref>PMID:25921071</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 3x1l" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[CRISPR subtype III-B (Cmr complex)\|CRISPR subtype III-B (Cmr complex)]]		*[[CRISPR subtype III-B (Cmr complex)\|CRISPR subtype III-B (Cmr complex)]]
	*[[CRISPR-Cas Part II\|CRISPR-Cas Part II]]		*[[CRISPR-Cas Part II\|CRISPR-Cas Part II]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Archaeoglobus fulgidus DSM 4304]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Pyrococcus furiosus COM1]]
		+	[[Category: Pyrococcus furiosus DSM 3638]]
		+	[[Category: Synthetic construct]]
	[[Category: Numata T]]		[[Category: Numata T]]
	[[Category: Osawa T]]		[[Category: Osawa T]]

OCA at 10:41, 31 August 2022

OCA — Wed, 31 Aug 2022 10:41:26 GMT

←Older revision		Revision as of 10:41, 31 August 2022
Line 1:		Line 1:

	==Crystal Structure of the CRISPR-Cas RNA Silencing Cmr Complex Bound to a Target Analog==		==Crystal Structure of the CRISPR-Cas RNA Silencing Cmr Complex Bound to a Target Analog==
-	<StructureSection load='3x1l' size='340' side='right'caption='[[3x1l]]~~, [[Resolution\|resolution]] 2.10Å~~' scene=''>	+	<StructureSection load='3x1l' size='340' side='right'caption='[[3x1l]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>~~[[3x1l]] is a 10 chain structure.~~ Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3X1L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3X1L FirstGlance]. <br>	+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3X1L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3X1L FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=3x1l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3x1l OCA], [https://pdbe.org/3x1l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3x1l RCSB], [https://www.ebi.ac.uk/pdbsum/3x1l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3x1l 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=3x1l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3x1l OCA], [https://pdbe.org/3x1l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3x1l RCSB], [https://www.ebi.ac.uk/pdbsum/3x1l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3x1l ProSAT]</span></td></tr>	+
	</table>		</table>
-	== Function ==
-	[[https://www.uniprot.org/uniprot/CMR5_ARCFU CMR5_ARCFU]] CRISPR (clustered regularly interspaced short palindromic repeat), is an adaptive immune system that provides protection against mobile genetic elements (viruses, transposable elements and conjugative plasmids). CRISPR clusters contain sequences complementary to antecedent mobile elements and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA). Part of the Cmr ribonucleoprotein complex (By similarity). [[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;">
-	== Publication Abstract from PubMed ==
-	In prokaryotes, Clustered regularly interspaced short palindromic repeat (CRISPR)-derived RNAs (crRNAs), together with CRISPR-associated (Cas) proteins, capture and degrade invading genetic materials. In the type III-B CRISPR-Cas system, six Cas proteins (Cmr1-Cmr6) and a crRNA form an RNA silencing Cmr complex. Here we report the 2.1 A crystal structure of the Cmr1-deficient, functional Cmr complex bound to single-stranded DNA, a substrate analog complementary to the crRNA guide. Cmr3 recognizes the crRNA 5' tag and defines the start position of the guide-target duplex, using its idiosyncratic loops. The beta-hairpins of three Cmr4 subunits intercalate within the duplex, causing nucleotide displacements with 6 nt intervals, and thus periodically placing the scissile bonds near the crucial aspartate of Cmr4. The structure reveals the mechanism for specifying the periodic target cleavage sites from the crRNA 5' tag and provides insights into the assembly of the type III interference machineries and the evolution of the Cmr and Cascade complexes.
-
-	Crystal Structure of the CRISPR-Cas RNA Silencing Cmr Complex Bound to a Target Analog.,Osawa T, Inanaga H, Sato C, Numata T Mol Cell. 2015 May 7;58(3):418-30. doi: 10.1016/j.molcel.2015.03.018. Epub 2015, Apr 23. PMID:25921071<ref>PMID:25921071</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 3x1l" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[CRISPR subtype III-B (Cmr complex)\|CRISPR subtype III-B (Cmr complex)]]		*[[CRISPR subtype III-B (Cmr complex)\|CRISPR subtype III-B (Cmr complex)]]
	*[[CRISPR-Cas Part II\|CRISPR-Cas Part II]]		*[[CRISPR-Cas Part II\|CRISPR-Cas Part II]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Numata, T]]	+	[[Category: Numata T]]
-	[[Category: Osawa, T]]	+	[[Category: Osawa T]]
-	~~[[Category: Rna binding]]~~	+
-	~~[[Category: Rna binding protein-rna-dna complex]]~~	+
-	~~[[Category: Rna silencing]]~~	+
-	~~[[Category: Rna-recognition motif~~]]	+

OCA at 05:01, 25 August 2022

OCA — Thu, 25 Aug 2022 05:01:20 GMT

←Older revision		Revision as of 05:01, 25 August 2022
Line 3:		Line 3:
	<StructureSection load='3x1l' size='340' side='right'caption='[[3x1l]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='3x1l' size='340' side='right'caption='[[3x1l]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3x1l]] is a 10 chain structure ~~with sequence from [https://en.wikipedia.org/wiki/Arcfu Arcfu] and [https://en.wikipedia.org/wiki/Pyrfu Pyrfu]~~. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3X1L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3X1L FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3x1l]] is a 10 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3X1L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3X1L FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=MG:MAGNESIUM+ION'>MG</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]), AF_1863 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224325 ARCFU]), AF_1861 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224325 ARCFU])</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=3x1l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3x1l OCA], [https://pdbe.org/3x1l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3x1l RCSB], [https://www.ebi.ac.uk/pdbsum/3x1l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3x1l 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=3x1l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3x1l OCA], [https://pdbe.org/3x1l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3x1l RCSB], [https://www.ebi.ac.uk/pdbsum/3x1l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3x1l ProSAT]</span></td></tr>
	</table>		</table>
Line 27:		Line 26:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Arcfu]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Pyrfu]]
	[[Category: Numata, T]]		[[Category: Numata, T]]
	[[Category: Osawa, T]]		[[Category: Osawa, T]]

OCA at 05:38, 10 August 2022

OCA — Wed, 10 Aug 2022 05:38:40 GMT

←Older revision		Revision as of 05:38, 10 August 2022
Line 1:		Line 1:

	==Crystal Structure of the CRISPR-Cas RNA Silencing Cmr Complex Bound to a Target Analog==		==Crystal Structure of the CRISPR-Cas RNA Silencing Cmr Complex Bound to a Target Analog==
-	<StructureSection load='3x1l' size='340' side='right' caption='[[3x1l]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='3x1l' size='340' side='right'caption='[[3x1l]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3x1l]] is a 10 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Arcfu Arcfu] and [~~http~~://en.wikipedia.org/wiki/Pyrfu Pyrfu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3X1L OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3X1L FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3x1l]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Arcfu Arcfu] and [https://en.wikipedia.org/wiki/Pyrfu Pyrfu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3X1L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3X1L FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=MG:MAGNESIUM+ION'>MG</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 ([~~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]), AF_1863 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224325 ARCFU]), AF_1861 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224325 ARCFU])</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]), AF_1863 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224325 ARCFU]), AF_1861 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224325 ARCFU])</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=3x1l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3x1l OCA], [~~http~~://pdbe.org/3x1l PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3x1l RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3x1l PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3x1l 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=3x1l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3x1l OCA], [https://pdbe.org/3x1l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3x1l RCSB], [https://www.ebi.ac.uk/pdbsum/3x1l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3x1l ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/CMR5_ARCFU CMR5_ARCFU]] CRISPR (clustered regularly interspaced short palindromic repeat), is an adaptive immune system that provides protection against mobile genetic elements (viruses, transposable elements and conjugative plasmids). CRISPR clusters contain sequences complementary to antecedent mobile elements and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA). Part of the Cmr ribonucleoprotein complex (By similarity). [[~~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/CMR5_ARCFU CMR5_ARCFU]] CRISPR (clustered regularly interspaced short palindromic repeat), is an adaptive immune system that provides protection against mobile genetic elements (viruses, transposable elements and conjugative plasmids). CRISPR clusters contain sequences complementary to antecedent mobile elements and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA). Part of the Cmr ribonucleoprotein complex (By similarity). [[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 28:		Line 28:
	</StructureSection>		</StructureSection>
	[[Category: Arcfu]]		[[Category: Arcfu]]
		+	[[Category: Large Structures]]
	[[Category: Pyrfu]]		[[Category: Pyrfu]]
	[[Category: Numata, T]]		[[Category: Numata, T]]

OCA at 17:09, 27 February 2019

OCA — Wed, 27 Feb 2019 17:09:05 GMT

←Older revision		Revision as of 17:09, 27 February 2019
Line 3:		Line 3:
	<StructureSection load='3x1l' size='340' side='right' caption='[[3x1l]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='3x1l' size='340' side='right' caption='[[3x1l]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3x1l]] is a 10 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3X1L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3X1L FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3x1l]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/Arcfu Arcfu] and [http://en.wikipedia.org/wiki/Pyrfu Pyrfu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3X1L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3X1L FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=MG:MAGNESIUM+ION'>MG</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 ([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]), AF_1863 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224325 ARCFU]), AF_1861 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=224325 ARCFU])</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=3x1l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3x1l OCA], [http://pdbe.org/3x1l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3x1l RCSB], [http://www.ebi.ac.uk/pdbsum/3x1l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3x1l 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=3x1l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3x1l OCA], [http://pdbe.org/3x1l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3x1l RCSB], [http://www.ebi.ac.uk/pdbsum/3x1l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3x1l ProSAT]</span></td></tr>
	</table>		</table>
Line 26:		Line 27:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Arcfu]]
		+	[[Category: Pyrfu]]
	[[Category: Numata, T]]		[[Category: Numata, T]]
	[[Category: Osawa, T]]		[[Category: Osawa, T]]

OCA at 17:36, 9 March 2017

OCA — Thu, 09 Mar 2017 17:36:29 GMT

←Older revision		Revision as of 17:36, 9 March 2017
Line 1:		Line 1:
		+
	==Crystal Structure of the CRISPR-Cas RNA Silencing Cmr Complex Bound to a Target Analog==		==Crystal Structure of the CRISPR-Cas RNA Silencing Cmr Complex Bound to a Target Analog==
	<StructureSection load='3x1l' size='340' side='right' caption='[[3x1l]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='3x1l' size='340' side='right' caption='[[3x1l]], [[Resolution\|resolution]] 2.10Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[3x1l]] is a 10 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3X1L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3X1L FirstGlance]. <br>		<table><tr><td colspan='2'>[[3x1l]] is a 10 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3X1L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3X1L FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3x1l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3x1l OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3x1l RCSB], [http://www.ebi.ac.uk/pdbsum/3x1l 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=3x1l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3x1l OCA], [http://pdbe.org/3x1l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3x1l RCSB], [http://www.ebi.ac.uk/pdbsum/3x1l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3x1l ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 16:		Line 17:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 3x1l" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[CRISPR subtype III-B (Cmr complex)\|CRISPR subtype III-B (Cmr complex)]]
		+	*[[CRISPR-Cas Part II\|CRISPR-Cas Part II]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 06:38, 20 May 2015

OCA — Wed, 20 May 2015 06:38:40 GMT

←Older revision		Revision as of 06:38, 20 May 2015
Line 1:		Line 1:
-	==Crystal ~~structure~~ of a Cas ~~protein~~==	+	==Crystal Structure of the CRISPR-Cas RNA Silencing Cmr Complex Bound to a Target Analog==
	<StructureSection load='3x1l' size='340' side='right' caption='[[3x1l]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='3x1l' size='340' side='right' caption='[[3x1l]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==

OCA at 12:18, 13 May 2015

OCA — Wed, 13 May 2015 12:18:20 GMT

←Older revision		Revision as of 12:18, 13 May 2015
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Crystal structure of a Cas protein==
		+	<StructureSection load='3x1l' size='340' side='right' caption='[[3x1l]], [[Resolution\|resolution]] 2.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3x1l]] is a 10 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3X1L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3X1L FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3x1l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3x1l OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3x1l RCSB], [http://www.ebi.ac.uk/pdbsum/3x1l PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/CMR5_ARCFU CMR5_ARCFU]] CRISPR (clustered regularly interspaced short palindromic repeat), is an adaptive immune system that provides protection against mobile genetic elements (viruses, transposable elements and conjugative plasmids). CRISPR clusters contain sequences complementary to antecedent mobile elements and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA). Part of the Cmr ribonucleoprotein complex (By similarity). [[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 ==
		+	In prokaryotes, Clustered regularly interspaced short palindromic repeat (CRISPR)-derived RNAs (crRNAs), together with CRISPR-associated (Cas) proteins, capture and degrade invading genetic materials. In the type III-B CRISPR-Cas system, six Cas proteins (Cmr1-Cmr6) and a crRNA form an RNA silencing Cmr complex. Here we report the 2.1 A crystal structure of the Cmr1-deficient, functional Cmr complex bound to single-stranded DNA, a substrate analog complementary to the crRNA guide. Cmr3 recognizes the crRNA 5' tag and defines the start position of the guide-target duplex, using its idiosyncratic loops. The beta-hairpins of three Cmr4 subunits intercalate within the duplex, causing nucleotide displacements with 6 nt intervals, and thus periodically placing the scissile bonds near the crucial aspartate of Cmr4. The structure reveals the mechanism for specifying the periodic target cleavage sites from the crRNA 5' tag and provides insights into the assembly of the type III interference machineries and the evolution of the Cmr and Cascade complexes.

-	~~The entry 3x1l is ON HOLD until Paper Publication~~	+	Crystal Structure of the CRISPR-Cas RNA Silencing Cmr Complex Bound to a Target Analog.,Osawa T, Inanaga H, Sato C, Numata T Mol Cell. 2015 May 7;58(3):418-30. doi: 10.1016/j.molcel.2015.03.018. Epub 2015, Apr 23. PMID:25921071<ref>PMID:25921071</ref>

-	~~Authors: Osawa~~, T.~~, Numata, T~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description: Crystal structure of a Cas protein~~	+	== References ==
-	~~[[Category: Unreleased Structures]]~~	+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Numata, T]]		[[Category: Numata, T]]
	[[Category: Osawa, T]]		[[Category: Osawa, T]]
		+	[[Category: Rna binding]]
		+	[[Category: Rna binding protein-rna-dna complex]]
		+	[[Category: Rna silencing]]
		+	[[Category: Rna-recognition motif]]

OCA at 13:14, 24 December 2014

OCA — Wed, 24 Dec 2014 13:14:30 GMT

←Older revision		Revision as of 13:14, 24 December 2014
Line 6:		Line 6:

	Description: Crystal structure of a Cas protein		Description: Crystal structure of a Cas protein
		+	[[Category: Unreleased Structures]]
		+	[[Category: Numata, T]]
		+	[[Category: Osawa, T]]

OCA at 12:51, 10 December 2014

OCA — Wed, 10 Dec 2014 12:51:42 GMT

←Older revision		Revision as of 12:51, 10 December 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3x1l is ON HOLD	+	The entry 3x1l is ON HOLD until Paper Publication

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

	Description: Crystal structure of a Cas protein		Description: Crystal structure of a Cas protein