5x2g - Revision history

OCA at 10:16, 27 March 2024

OCA — Wed, 27 Mar 2024 10:16:54 GMT

←Older revision		Revision as of 10:16, 27 March 2024
Line 3:		Line 3:
	<StructureSection load='5x2g' size='340' side='right'caption='[[5x2g]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='5x2g' size='340' side='right'caption='[[5x2g]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5x2g]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Camje Camje~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X2G OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5X2G FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5x2g]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Campylobacter_jejuni Campylobacter jejuni], [https://en.wikipedia.org/wiki/Campylobacter_jejuni_subsp._jejuni_NCTC_11168_=_ATCC_700819 Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819] 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=5X2G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5X2G 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>~~</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]] 2.4Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[5x2h\|5x2h]]</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></td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~"><~~b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">cas9, Cj1523c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=192222 CAMJE])~~</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=5x2g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x2g OCA], [https://pdbe.org/5x2g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5x2g RCSB], [https://www.ebi.ac.uk/pdbsum/5x2g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5x2g 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=5x2g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x2g OCA], [~~http~~://pdbe.org/5x2g PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5x2g RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5x2g PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5x2g ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/CAS9_CAMJE CAS9_CAMJE]] 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 spacers, sequences complementary to antecedent mobile elements, and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA). In type II CRISPR systems correct processing of pre-crRNA requires a trans-encoded small RNA (tracrRNA), endogenous ribonuclease 3 (rnc) and this protein. The tracrRNA serves as a guide for ribonuclease 3-aided processing of pre-crRNA. Subsequently Cas9/crRNA/tracrRNA endonucleolytically cleaves linear or circular dsDNA target complementary to the spacer; Cas9 is inactive in the absence of the 2 guide RNAs (gRNA). Cas9 recognizes the protospacer adjacent motif (PAM) in the CRISPR repeat sequences to help distinguish self versus nonself, as targets within the bacterial CRISPR locus do not have PAMs. PAM recognition is also required for catalytic activity (By similarity). Cuts target DNA in Cas9:gRNAs mixing experiments with N.meningitidis strain Z2491 and P.multocoda strain Pm70.[HAMAP-Rule:MF_01480]<ref>PMID:24270795</ref>	+	[https://www.uniprot.org/uniprot/CAS9_CAMJE CAS9_CAMJE] 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 spacers, sequences complementary to antecedent mobile elements, and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA). In type II CRISPR systems correct processing of pre-crRNA requires a trans-encoded small RNA (tracrRNA), endogenous ribonuclease 3 (rnc) and this protein. The tracrRNA serves as a guide for ribonuclease 3-aided processing of pre-crRNA. Subsequently Cas9/crRNA/tracrRNA endonucleolytically cleaves linear or circular dsDNA target complementary to the spacer; Cas9 is inactive in the absence of the 2 guide RNAs (gRNA). Cas9 recognizes the protospacer adjacent motif (PAM) in the CRISPR repeat sequences to help distinguish self versus nonself, as targets within the bacterial CRISPR locus do not have PAMs. PAM recognition is also required for catalytic activity (By similarity). Cuts target DNA in Cas9:gRNAs mixing experiments with N.meningitidis strain Z2491 and P.multocoda strain Pm70.[HAMAP-Rule:MF_01480]<ref>PMID:24270795</ref>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	The RNA-guided endonuclease Cas9 generates a double-strand break at DNA target sites complementary to the guide RNA and has been harnessed for the development of a variety of new technologies, such as genome editing. Here, we report the crystal structures of Campylobacter jejuni Cas9 (CjCas9), one of the smallest Cas9 orthologs, in complex with an sgRNA and its target DNA. The structures provided insights into a minimal Cas9 scaffold and revealed the remarkable mechanistic diversity of the CRISPR-Cas9 systems. The CjCas9 guide RNA contains a triple-helix structure, which is distinct from known RNA triple helices, thereby expanding the natural repertoire of RNA triple helices. Furthermore, unlike the other Cas9 orthologs, CjCas9 contacts the nucleotide sequences in both the target and non-target DNA strands and recognizes the 5'-NNNVRYM-3' as the protospacer-adjacent motif. Collectively, these findings improve our mechanistic understanding of the CRISPR-Cas9 systems and may facilitate Cas9 engineering.	+
-		+
-	Crystal Structure of the Minimal Cas9 from Campylobacter jejuni Reveals the Molecular Diversity in the CRISPR-Cas9 Systems.,Yamada M, Watanabe Y, Gootenberg JS, Hirano H, Ran FA, Nakane T, Ishitani R, Zhang F, Nishimasu H, Nureki O Mol Cell. 2017 Mar 16;65(6):1109-1121.e3. doi: 10.1016/j.molcel.2017.02.007. PMID:28306506<ref>PMID:28306506</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 5x2g" style="background-color:#fffaf0;"></div~~>	+

	==See Also==		==See Also==
Line 27:		Line 17:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Camje~~]]	+	[[Category: Campylobacter jejuni]]
		+	[[Category: Campylobacter jejuni subsp. jejuni NCTC 11168 = ATCC 700819]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Hirano, H]]	+	[[Category: Synthetic construct]]
-	[[Category: Ishitani, R]]	+	[[Category: Hirano H]]
-	[[Category: Nakane, T]]	+	[[Category: Ishitani R]]
-	[[Category: Nishimasu, H]]	+	[[Category: Nakane T]]
-	[[Category: Nureki, O]]	+	[[Category: Nishimasu H]]
-	[[Category: Watanabe, Y]]	+	[[Category: Nureki O]]
-	[[Category: Yamada, M]]	+	[[Category: Watanabe Y]]
-	~~[[Category: Complex]]~~	+	[[Category: Yamada M]]
-	~~[[Category: Crispr-cas9]]~~	+
-	~~[[Category: Dna]]~~	+
-	~~[[Category: Hydrolase-rna-dna complex]]~~	+
-	~~[[Category: Nuclease]]~~	+
-	~~[[Category: Rna~~]]	+

OCA at 07:22, 7 October 2020

OCA — Wed, 07 Oct 2020 07:22:31 GMT

←Older revision		Revision as of 07:22, 7 October 2020
Line 1:		Line 1:

	==Crystal structure of Campylobacter jejuni Cas9 in complex with sgRNA and target DNA (AGAAACC PAM)==		==Crystal structure of Campylobacter jejuni Cas9 in complex with sgRNA and target DNA (AGAAACC PAM)==
-	<StructureSection load='5x2g' size='340' side='right' caption='[[5x2g]], [[Resolution\|resolution]] 2.40Å' scene=''>	+	<StructureSection load='5x2g' size='340' side='right'caption='[[5x2g]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5x2g]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X2G OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5X2G FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5x2g]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Camje Camje]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X2G OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5X2G 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></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></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5x2h\|5x2h]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5x2h\|5x2h]]</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=5x2g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x2g OCA], [http://pdbe.org/5x2g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x2g RCSB], [http://www.ebi.ac.uk/pdbsum/5x2g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x2g ProSAT]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">cas9, Cj1523c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=192222 CAMJE])</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=5x2g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x2g OCA], [http://pdbe.org/5x2g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x2g RCSB], [http://www.ebi.ac.uk/pdbsum/5x2g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x2g ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 5x2g" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5x2g" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Endonuclease 3D structures\|Endonuclease 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Camje]]
		+	[[Category: Large Structures]]
	[[Category: Hirano, H]]		[[Category: Hirano, H]]
	[[Category: Ishitani, R]]		[[Category: Ishitani, R]]

OCA at 14:06, 29 March 2017

OCA — Wed, 29 Mar 2017 14:06:42 GMT

←Older revision		Revision as of 14:06, 29 March 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5x2g is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Crystal structure of Campylobacter jejuni Cas9 in complex with sgRNA and target DNA (AGAAACC PAM)==
		+	<StructureSection load='5x2g' size='340' side='right' caption='[[5x2g]], [[Resolution\|resolution]] 2.40Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5x2g]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5X2G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5X2G 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></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5x2h\|5x2h]]</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=5x2g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5x2g OCA], [http://pdbe.org/5x2g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5x2g RCSB], [http://www.ebi.ac.uk/pdbsum/5x2g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5x2g ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/CAS9_CAMJE CAS9_CAMJE]] 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 spacers, sequences complementary to antecedent mobile elements, and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA). In type II CRISPR systems correct processing of pre-crRNA requires a trans-encoded small RNA (tracrRNA), endogenous ribonuclease 3 (rnc) and this protein. The tracrRNA serves as a guide for ribonuclease 3-aided processing of pre-crRNA. Subsequently Cas9/crRNA/tracrRNA endonucleolytically cleaves linear or circular dsDNA target complementary to the spacer; Cas9 is inactive in the absence of the 2 guide RNAs (gRNA). Cas9 recognizes the protospacer adjacent motif (PAM) in the CRISPR repeat sequences to help distinguish self versus nonself, as targets within the bacterial CRISPR locus do not have PAMs. PAM recognition is also required for catalytic activity (By similarity). Cuts target DNA in Cas9:gRNAs mixing experiments with N.meningitidis strain Z2491 and P.multocoda strain Pm70.[HAMAP-Rule:MF_01480]<ref>PMID:24270795</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The RNA-guided endonuclease Cas9 generates a double-strand break at DNA target sites complementary to the guide RNA and has been harnessed for the development of a variety of new technologies, such as genome editing. Here, we report the crystal structures of Campylobacter jejuni Cas9 (CjCas9), one of the smallest Cas9 orthologs, in complex with an sgRNA and its target DNA. The structures provided insights into a minimal Cas9 scaffold and revealed the remarkable mechanistic diversity of the CRISPR-Cas9 systems. The CjCas9 guide RNA contains a triple-helix structure, which is distinct from known RNA triple helices, thereby expanding the natural repertoire of RNA triple helices. Furthermore, unlike the other Cas9 orthologs, CjCas9 contacts the nucleotide sequences in both the target and non-target DNA strands and recognizes the 5'-NNNVRYM-3' as the protospacer-adjacent motif. Collectively, these findings improve our mechanistic understanding of the CRISPR-Cas9 systems and may facilitate Cas9 engineering.

-	~~Authors:~~ Yamada, M., Watanabe, Y., Hirano, H., ~~Nakane~~, T., Ishitani, R., ~~Nishimasu~~, H., Nureki, O.	+	Crystal Structure of the Minimal Cas9 from Campylobacter jejuni Reveals the Molecular Diversity in the CRISPR-Cas9 Systems.,Yamada M, Watanabe Y, Gootenberg JS, Hirano H, Ran FA, Nakane T, Ishitani R, Zhang F, Nishimasu H, Nureki O Mol Cell. 2017 Mar 16;65(6):1109-1121.e3. doi: 10.1016/j.molcel.2017.02.007. PMID:28306506<ref>PMID:28306506</ref>

-	~~Description: Crystal structure~~ of ~~Campylobacter jejuni Cas9 in complex with sgRNA and target DNA (AGAAACC PAM)~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Nureki, O]]~~	+	<div class="pdbe-citations 5x2g" style="background-color:#fffaf0;"></div>
-	~~[[Category: Nishimasu, H]]~~	+	== References ==
-	~~[[Category: Ishitani, R]]~~	+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Hirano, H]]		[[Category: Hirano, H]]
-	[[Category: ~~Watanabe~~, Y]]	+	[[Category: Ishitani, R]]
	[[Category: Nakane, T]]		[[Category: Nakane, T]]
		+	[[Category: Nishimasu, H]]
		+	[[Category: Nureki, O]]
		+	[[Category: Watanabe, Y]]
	[[Category: Yamada, M]]		[[Category: Yamada, M]]
		+	[[Category: Complex]]
		+	[[Category: Crispr-cas9]]
		+	[[Category: Dna]]
		+	[[Category: Hydrolase-rna-dna complex]]
		+	[[Category: Nuclease]]
		+	[[Category: Rna]]

OCA at 20:06, 15 March 2017

OCA — Wed, 15 Mar 2017 20:06:46 GMT

←Older revision		Revision as of 20:06, 15 March 2017
Line 9:		Line 9:
	[[Category: Nureki, O]]		[[Category: Nureki, O]]
	[[Category: Nishimasu, H]]		[[Category: Nishimasu, H]]
-	[[Category: Hirano, H]]
-	[[Category: Yamada, M]]
	[[Category: Ishitani, R]]		[[Category: Ishitani, R]]
		+	[[Category: Hirano, H]]
	[[Category: Watanabe, Y]]		[[Category: Watanabe, Y]]
	[[Category: Nakane, T]]		[[Category: Nakane, T]]
		+	[[Category: Yamada, M]]

OCA: Protected "5x2g" [edit=sysop:move=sysop]

OCA — Thu, 09 Mar 2017 15:36:46 GMT

Protected "5x2g" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:36, 9 March 2017

OCA: New page: '''Unreleased structure''' The entry 5x2g is ON HOLD until Paper Publication Authors: Yamada, M., Watanabe, Y., Hirano, H., Nakane, T., Ishitani, R., Nishimasu, H., Nureki, O. Descript...

OCA — Thu, 09 Mar 2017 15:36:44 GMT

New page: '''Unreleased structure''' The entry 5x2g is ON HOLD until Paper Publication Authors: Yamada, M., Watanabe, Y., Hirano, H., Nakane, T., Ishitani, R., Nishimasu, H., Nureki, O. Descript...

New page

'''Unreleased structure'''

The entry 5x2g is ON HOLD until Paper Publication

Authors: Yamada, M., Watanabe, Y., Hirano, H., Nakane, T., Ishitani, R., Nishimasu, H., Nureki, O.

Description: Crystal structure of Campylobacter jejuni Cas9 in complex with sgRNA and target DNA (AGAAACC PAM)
[[Category: Unreleased Structures]]
[[Category: Nureki, O]]
[[Category: Nishimasu, H]]
[[Category: Hirano, H]]
[[Category: Yamada, M]]
[[Category: Ishitani, R]]
[[Category: Watanabe, Y]]
[[Category: Nakane, T]]