5xus - Revision history

OCA at 08:14, 22 November 2023

OCA — Wed, 22 Nov 2023 08:14:24 GMT

←Older revision		Revision as of 08:14, 22 November 2023
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	<StructureSection load='5xus' size='340' side='right'caption='[[5xus]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='5xus' size='340' side='right'caption='[[5xus]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xus]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Lachnospiraceae_bacterium_nd2006~~ Lachnospiraceae bacterium ~~nd2006~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XUS OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5XUS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xus]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Lachnospiraceae_bacterium_ND2006 Lachnospiraceae bacterium ND2006] 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=5XUS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XUS FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 2.5Å</td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5xus FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xus OCA], [~~http~~://pdbe.org/5xus PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5xus RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5xus PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5xus ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=5xus FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xus OCA], [https://pdbe.org/5xus PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xus RCSB], [https://www.ebi.ac.uk/pdbsum/5xus PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xus ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/A0A182DWE3_9FIRM A0A182DWE3_9FIRM]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Lachnospiraceae bacterium ~~nd2006~~]]	+	[[Category: Lachnospiraceae bacterium ND2006]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Ishitani, R]]	+	[[Category: Synthetic construct]]
-	[[Category: Nishimasu, H]]	+	[[Category: Ishitani R]]
-	[[Category: Nureki, O]]	+	[[Category: Nishimasu H]]
-	[[Category: Yamano, T]]	+	[[Category: Nureki O]]
-	~~[[Category: Hydrolase-rna-dna complex]]~~	+	[[Category: Yamano T]]
-	~~[[Category: Nuclease~~]]	+

OCA at 06:59, 14 October 2020

OCA — Wed, 14 Oct 2020 06:59:12 GMT

←Older revision		Revision as of 06:59, 14 October 2020
Line 1:		Line 1:

	==Crystal structure of Lachnospiraceae bacterium ND2006 Cpf1 in complex with crRNA and target DNA (TTTA PAM)==		==Crystal structure of Lachnospiraceae bacterium ND2006 Cpf1 in complex with crRNA and target DNA (TTTA PAM)==
-	<StructureSection load='5xus' size='340' side='right' caption='[[5xus]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='5xus' size='340' side='right'caption='[[5xus]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xus]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Lachnospiraceae_bacterium_nd2006 Lachnospiraceae bacterium nd2006]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XUS OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5XUS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xus]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Lachnospiraceae_bacterium_nd2006 Lachnospiraceae bacterium nd2006]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XUS OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5XUS FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=5xus FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xus OCA], [http://pdbe.org/5xus PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xus RCSB], [http://www.ebi.ac.uk/pdbsum/5xus PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xus ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5xus FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xus OCA], [http://pdbe.org/5xus PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xus RCSB], [http://www.ebi.ac.uk/pdbsum/5xus PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xus ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	</StructureSection>		</StructureSection>
	[[Category: Lachnospiraceae bacterium nd2006]]		[[Category: Lachnospiraceae bacterium nd2006]]
		+	[[Category: Large Structures]]
	[[Category: Ishitani, R]]		[[Category: Ishitani, R]]
	[[Category: Nishimasu, H]]		[[Category: Nishimasu, H]]

OCA at 07:57, 6 December 2017

OCA — Wed, 06 Dec 2017 07:57:21 GMT

←Older revision		Revision as of 07:57, 6 December 2017
Line 3:		Line 3:
	<StructureSection load='5xus' size='340' side='right' caption='[[5xus]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='5xus' size='340' side='right' caption='[[5xus]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5xus]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XUS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XUS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5xus]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Lachnospiraceae_bacterium_nd2006 Lachnospiraceae bacterium nd2006]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XUS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XUS FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=5xus FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xus OCA], [http://pdbe.org/5xus PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xus RCSB], [http://www.ebi.ac.uk/pdbsum/5xus PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xus 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=5xus FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xus OCA], [http://pdbe.org/5xus PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xus RCSB], [http://www.ebi.ac.uk/pdbsum/5xus PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xus ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The RNA-guided Cpf1 (also known as Cas12a) nuclease associates with a CRISPR RNA (crRNA) and cleaves the double-stranded DNA target complementary to the crRNA guide. The two Cpf1 orthologs from Acidaminococcus sp. (AsCpf1) and Lachnospiraceae bacterium (LbCpf1) have been harnessed for eukaryotic genome editing. Cpf1 requires a specific nucleotide sequence, called a protospacer adjacent motif (PAM), for target recognition. Besides the canonical TTTV PAM, Cpf1 recognizes suboptimal C-containing PAMs. Here, we report four crystal structures of LbCpf1 in complex with the crRNA and its target DNA containing either TTTA, TCTA, TCCA, or CCCA as the PAM. These structures revealed that, depending on the PAM sequences, LbCpf1 undergoes conformational changes to form altered interactions with the PAM-containing DNA duplexes, thereby achieving the relaxed PAM recognition. Collectively, the present structures advance our mechanistic understanding of the PAM-dependent, crRNA-guided DNA cleavage by the Cpf1 family nucleases.
		+
		+	Structural Basis for the Canonical and Non-canonical PAM Recognition by CRISPR-Cpf1.,Yamano T, Zetsche B, Ishitani R, Zhang F, Nishimasu H, Nureki O Mol Cell. 2017 Aug 17;67(4):633-645.e3. doi: 10.1016/j.molcel.2017.06.035. Epub, 2017 Aug 3. PMID:28781234<ref>PMID:28781234</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5xus" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Lachnospiraceae bacterium nd2006]]
	[[Category: Ishitani, R]]		[[Category: Ishitani, R]]
	[[Category: Nishimasu, H]]		[[Category: Nishimasu, H]]

OCA: Protected "5xus" [edit=sysop:move=sysop]

OCA — Sat, 07 Oct 2017 11:12:29 GMT

Protected "5xus" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:12, 7 October 2017

OCA: New page: ==Crystal structure of Lachnospiraceae bacterium ND2006 Cpf1 in complex with crRNA and target DNA (TTTA PAM)== == Structural highlights ==
<table><tr><td colspan='2'>[[5xus]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XUS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5XUS FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=5xus FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xus OCA], [http://pdbe.org/5xus PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xus RCSB], [http://www.ebi.ac.uk/pdbsum/5xus PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xus ProSAT]</span></td></tr>
</table>
TOC
</StructureSection>
[[Category: Ishitani, R]]
[[Category: Nishimasu, H]]
[[Category: Nureki, O]]
[[Category: Yamano, T]]
[[Category: Hydrolase-rna-dna complex]]
[[Category: Nuclease]]