4lb6 - Revision history

OCA at 16:15, 20 September 2023

OCA — Wed, 20 Sep 2023 16:15:52 GMT

←Older revision		Revision as of 16:15, 20 September 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4lb6]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Danio_rerio Danio rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LB6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4LB6 FirstGlance]. <br>		<table><tr><td colspan='2'>[[4lb6]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Danio_rerio Danio rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LB6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4LB6 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=4lb6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lb6 OCA], [https://pdbe.org/4lb6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4lb6 RCSB], [https://www.ebi.ac.uk/pdbsum/4lb6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4lb6 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]] 1.8Å</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=4lb6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lb6 OCA], [https://pdbe.org/4lb6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4lb6 RCSB], [https://www.ebi.ac.uk/pdbsum/4lb6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4lb6 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 10:49, 14 December 2022

OCA — Wed, 14 Dec 2022 10:49:29 GMT

←Older revision		Revision as of 10:49, 14 December 2022
Line 1:		Line 1:

	==Crystal structure of PKZ Zalpha in complex with ds(CG)6 (tetragonal form)==		==Crystal structure of PKZ Zalpha in complex with ds(CG)6 (tetragonal form)==
-	<StructureSection load='4lb6' size='340' side='right' caption='[[4lb6]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='4lb6' size='340' side='right'caption='[[4lb6]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4lb6]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Brachidanio_rerio Brachidanio~~ rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LB6 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4LB6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4lb6]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Danio_rerio Danio rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LB6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4LB6 FirstGlance]. <br>
-	</td></tr>~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4lb5\|4lb5]]</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=4lb6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lb6 OCA], [https://pdbe.org/4lb6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4lb6 RCSB], [https://www.ebi.ac.uk/pdbsum/4lb6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4lb6 ProSAT]</span></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pkz ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7955 Brachidanio rerio])</td></tr>	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Non-specific_serine/threonine_protein_kinase Non-specific serine/threonine protein kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.11.1 2.7.11.1] </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=4lb6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lb6 OCA], [~~http~~://pdbe.org/4lb6 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4lb6 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4lb6 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4lb6 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q5NE14_DANRE Q5NE14_DANRE]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Brachidanio~~ rerio]]	+	[[Category: Danio rerio]]
-	[[Category: ~~Non-specific serine/threonine protein kinase~~]]	+	[[Category: Large Structures]]
-	[[Category: Athanasiadis, A]]	+	[[Category: Athanasiadis A]]
-	[[Category: Rosa, M De]]	+	[[Category: De Rosa M]]
-	[[Category: Zacarias, S]]	+	[[Category: Zacarias S]]
-	~~[[Category: Eif2a]]~~	+
-	~~[[Category: Innate immunity]]~~	+
-	~~[[Category: Kinase]]~~	+
-	~~[[Category: Transferase-dna complex]]~~	+
-	~~[[Category: Whth]]~~	+
-	~~[[Category: Z-dna]]~~	+
-	~~[[Category: Z-rna]]~~	+
-	~~[[Category: Zalpha]]~~	+
-	~~[[Category: Zbd~~]]	+

OCA at 00:17, 5 August 2016

OCA — Fri, 05 Aug 2016 00:17:40 GMT

←Older revision		Revision as of 00:17, 5 August 2016
Line 1:		Line 1:
-	{{STRUCTURE_4lb6\| PDB=4lb6 \| SCENE= }}
-	===Crystal structure of PKZ Zalpha in complex with ds(CG)6 (tetragonal form)===
-	{{ABSTRACT_PUBMED_23975196}}

-	==~~About this Structure~~==	+	==Crystal structure of PKZ Zalpha in complex with ds(CG)6 (tetragonal form)==
-	[[4lb6]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Brachidanio_rerio Brachidanio rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LB6 OCA].	+	<StructureSection load='4lb6' size='340' side='right' caption='[[4lb6]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4lb6]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Brachidanio_rerio Brachidanio rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LB6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4LB6 FirstGlance]. <br>
		+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4lb5\|4lb5]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">pkz ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=7955 Brachidanio rerio])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Non-specific_serine/threonine_protein_kinase Non-specific serine/threonine protein kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.11.1 2.7.11.1] </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=4lb6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lb6 OCA], [http://pdbe.org/4lb6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4lb6 RCSB], [http://www.ebi.ac.uk/pdbsum/4lb6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4lb6 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The RNA-dependent protein kinase PKR plays a central role in the antiviral defense of vertebrates by shutting down protein translation upon detection of viral dsRNA in the cytoplasm. In some teleost fish, PKZ, a homolog of PKR, performs the same function, but surprisingly, instead of dsRNA binding domains, it harbors two Z-DNA/Z-RNA-binding domains belonging to the Zalpha domain family. Zalpha domains have also been found in other proteins, which have key roles in the regulation of interferon responses such as ADAR1 and DNA-dependent activator of IFN-regulatory factors (DAI) and in viral proteins involved in immune response evasion such as the poxviral E3L and the Cyprinid Herpesvirus 3 ORF112. The underlying mechanism of nucleic acids binding and stabilization by Zalpha domains is still unclear. Here, we present two crystal structures of the zebrafish PKZ Zalpha domain (DrZalphaPKZ) in alternatively organized complexes with a (CG)6 DNA oligonucleotide at 2 and 1.8 A resolution. These structures reveal novel aspects of the Zalpha interaction with DNA, and they give insights on the arrangement of multiple Zalpha domains on DNA helices longer than the minimal binding site.

-	~~==Reference==~~	+	Structural basis for Z-DNA binding and stabilization by the zebrafish Z-DNA dependent protein kinase PKZ.,de Rosa M, Zacarias S, Athanasiadis A Nucleic Acids Res. 2013 Aug 23. PMID:23975196<ref>PMID:23975196</ref>
-	<ref ~~group="xtra"~~>PMID:~~023975196~~</ref><~~references group~~="~~xtra~~"/><references/>	+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 4lb6" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Brachidanio rerio]]		[[Category: Brachidanio rerio]]
	[[Category: Non-specific serine/threonine protein kinase]]		[[Category: Non-specific serine/threonine protein kinase]]
-	[[Category: Athanasiadis, A.]]	+	[[Category: Athanasiadis, A]]
-	[[Category: Rosa, M De.]]	+	[[Category: Rosa, M De]]
-	[[Category: Zacarias, S.]]	+	[[Category: Zacarias, S]]
	[[Category: Eif2a]]		[[Category: Eif2a]]
	[[Category: Innate immunity]]		[[Category: Innate immunity]]

OCA at 06:00, 4 December 2013

OCA — Wed, 04 Dec 2013 06:00:35 GMT

←Older revision		Revision as of 06:00, 4 December 2013
Line 4:		Line 4:

	==About this Structure==		==About this Structure==
-	[[4lb6]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Danio_rerio Danio~~ rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LB6 OCA].	+	[[4lb6]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Brachidanio_rerio Brachidanio rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LB6 OCA].

	==Reference==		==Reference==
	<ref group="xtra">PMID:023975196</ref><references group="xtra"/><references/>		<ref group="xtra">PMID:023975196</ref><references group="xtra"/><references/>
-	[[Category: ~~Danio~~ rerio]]	+	[[Category: Brachidanio rerio]]
	[[Category: Non-specific serine/threonine protein kinase]]		[[Category: Non-specific serine/threonine protein kinase]]
	[[Category: Athanasiadis, A.]]		[[Category: Athanasiadis, A.]]

OCA at 04:09, 20 September 2013

OCA — Fri, 20 Sep 2013 04:09:12 GMT

←Older revision		Revision as of 04:09, 20 September 2013
Line 1:		Line 1:
-	~~'''Unreleased~~ structure~~'''~~	+	{{STRUCTURE_4lb6\| PDB=4lb6 \| SCENE= }}
		+	===Crystal structure of PKZ Zalpha in complex with ds(CG)6 (tetragonal form)===
		+	{{ABSTRACT_PUBMED_23975196}}

-	~~The entry~~ 4lb6 is ~~ON HOLD~~	+	==About this Structure==
		+	[[4lb6]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Danio_rerio Danio rerio]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LB6 OCA].

-	~~Authors~~: De Rosa, M., Zacarias, S.~~, Athanasiadis, A.~~	+	==Reference==
-		+	<ref group="xtra">PMID:023975196</ref><references group="xtra"/><references/>
-	~~Description~~: ~~Crystal structure of PKZ Zalpha in~~ complex ~~with ds(CG)6 (tetragonal form)~~	+	[[Category: Danio rerio]]
		+	[[Category: Non-specific serine/threonine protein kinase]]
		+	[[Category: Athanasiadis, A.]]
		+	[[Category: Rosa, M De.]]
		+	[[Category: Zacarias, S.]]
		+	[[Category: Eif2a]]
		+	[[Category: Innate immunity]]
		+	[[Category: Kinase]]
		+	[[Category: Transferase-dna complex]]
		+	[[Category: Whth]]
		+	[[Category: Z-dna]]
		+	[[Category: Z-rna]]
		+	[[Category: Zalpha]]
		+	[[Category: Zbd]]

OCA at 04:15, 1 August 2013

OCA — Thu, 01 Aug 2013 04:15:37 GMT

←Older revision		Revision as of 04:15, 1 August 2013
Line 3:		Line 3:
	The entry 4lb6 is ON HOLD		The entry 4lb6 is ON HOLD

-	Authors: de Rosa, M., Zacarias, S., Athanasiadis, A.	+	Authors: De Rosa, M., Zacarias, S., Athanasiadis, A.

	Description: Crystal structure of PKZ Zalpha in complex with ds(CG)6 (tetragonal form)		Description: Crystal structure of PKZ Zalpha in complex with ds(CG)6 (tetragonal form)

OCA: Protected "4lb6" [edit=sysop:move=sysop]

OCA — Sun, 30 Jun 2013 09:12:27 GMT

Protected "4lb6" [edit=sysop:move=sysop]

←Older revision

Revision as of 09:12, 30 June 2013

OCA: New page: '''Unreleased structure''' The entry 4lb6 is ON HOLD Authors: de Rosa, M., Zacarias, S., Athanasiadis, A. Description: Crystal structure of PKZ Zalpha in complex with ds(CG)6 (tetragon...

OCA — Sun, 30 Jun 2013 09:12:26 GMT

New page: '''Unreleased structure''' The entry 4lb6 is ON HOLD Authors: de Rosa, M., Zacarias, S., Athanasiadis, A. Description: Crystal structure of PKZ Zalpha in complex with ds(CG)6 (tetragon...

New page

'''Unreleased structure'''

The entry 4lb6 is ON HOLD

Authors: de Rosa, M., Zacarias, S., Athanasiadis, A.

Description: Crystal structure of PKZ Zalpha in complex with ds(CG)6 (tetragonal form)