5oqz - Revision history

OCA at 16:58, 13 December 2023

OCA — Wed, 13 Dec 2023 16:58:35 GMT

←Older revision		Revision as of 16:58, 13 December 2023
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	<StructureSection load='5oqz' size='340' side='right'caption='[[5oqz]], [[Resolution\|resolution]] 0.81Å' scene=''>		<StructureSection load='5oqz' size='340' side='right'caption='[[5oqz]], [[Resolution\|resolution]] 0.81Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5oqz]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Rubgi Rubgi~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OQZ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5OQZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5oqz]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Rubrivivax_gelatinosus_IL144 Rubrivivax gelatinosus IL144]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OQZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5OQZ FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~RGE_06990 (~~[~~http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=983917 RUBGI])~~</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]] 0.806Å</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=5oqz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5oqz OCA], [~~http~~://pdbe.org/5oqz PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5oqz RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5oqz PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5oqz 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=5oqz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5oqz OCA], [https://pdbe.org/5oqz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5oqz RCSB], [https://www.ebi.ac.uk/pdbsum/5oqz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5oqz ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/I0HM07_RUBGI I0HM07_RUBGI]
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Rubgi~~]]	+	[[Category: Rubrivivax gelatinosus IL144]]
-	[[Category: Fage~~, C D~~]]	+	[[Category: Fage CD]]
-	[[Category: Hegemann~~, J D~~]]	+	[[Category: Hegemann JD]]
-	[[Category: Marahiel~~, M A]]~~	+	[[Category: Marahiel MA]]
-	~~[[Category: Lasso peptide]]~~	+
-	~~[[Category: Ribosomally synthesized and post-translationally modified peptide]]~~	+
-	~~[[Category: Ripp]]~~	+
-	~~[[Category: Unknown function~~]]	+

OCA at 13:18, 10 May 2019

OCA — Fri, 10 May 2019 13:18:47 GMT

←Older revision		Revision as of 13:18, 10 May 2019
Line 1:		Line 1:

	==Crystal structure of the lasso peptide rubrivinodin==		==Crystal structure of the lasso peptide rubrivinodin==
-	<StructureSection load='5oqz' size='340' side='right' caption='[[5oqz]], [[Resolution\|resolution]] 0.81Å' scene=''>	+	<StructureSection load='5oqz' size='340' side='right'caption='[[5oqz]], [[Resolution\|resolution]] 0.81Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5oqz]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Rubgi Rubgi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OQZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OQZ FirstGlance]. <br>		<table><tr><td colspan='2'>[[5oqz]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Rubgi Rubgi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OQZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OQZ FirstGlance]. <br>
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Rubgi]]		[[Category: Rubgi]]
	[[Category: Fage, C D]]		[[Category: Fage, C D]]

OCA at 06:57, 15 February 2018

OCA — Thu, 15 Feb 2018 06:57:32 GMT

←Older revision		Revision as of 06:57, 15 February 2018
Line 3:		Line 3:
	<StructureSection load='5oqz' size='340' side='right' caption='[[5oqz]], [[Resolution\|resolution]] 0.81Å' scene=''>		<StructureSection load='5oqz' size='340' side='right' caption='[[5oqz]], [[Resolution\|resolution]] 0.81Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5oqz]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OQZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OQZ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5oqz]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Rubgi Rubgi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OQZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OQZ 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=5oqz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5oqz OCA], [http://pdbe.org/5oqz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5oqz RCSB], [http://www.ebi.ac.uk/pdbsum/5oqz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5oqz ProSAT]</span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RGE_06990 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=983917 RUBGI])</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=5oqz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5oqz OCA], [http://pdbe.org/5oqz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5oqz RCSB], [http://www.ebi.ac.uk/pdbsum/5oqz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5oqz ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Lasso peptides constitute a structurally unique class of ribosomally synthesized and post-translationally modified peptides (RiPPs) characterized by a mechanically interlocked structure in which the C-terminal tail of the peptide is threaded and trapped within an N-terminal macrolactam ring. Tandem mass spectrometry using collision induced dissociation (CID) and electron capture dissociation (ECD) have shown previously different fragmentation patterns for capistruin, microcin J25 and their corresponding branched-cyclic forms in which the C-terminal tail is unthreaded. In order to develop general rules that unambiguously discriminate the lasso and branched-cyclic topologies, this report presents experimental evidence for a set of twenty-one lasso peptides analyzed by CID and electron transfer dissociation (ETD). CID experiments on lasso peptides specifically yielded mechanically interlocked species with associated bi and yj fragments. For class II lasso peptides, these lasso-specific fragments were observed only for peptides in which the loop, located above the macrolactam ring, was strictly longer than four amino acid residues. For class I and III lasso peptides, part of the C-terminal tail remains covalently linked to the macrolactam ring by disulfide bonds; associated bi and yj fragments therefore do not clearly constitute a signature of the lasso topology. ETD experiments of lasso peptides showed a significant increase of hydrogen migration events in the loop region when compared to their branched-cyclic topoisomers, leading to the formation of specific ci /z'j fragments for all lasso peptides, regardless of their class and loop size. Our experiments enabled us to establish general rules for obtaining structural details from CID and ETD fragmentation patterns, obviating the need for structure determination by NMR or X-ray crystallography.
		+
		+	General rules of fragmentation evidencing lasso structures in CID and ETD.,Jeanne Dit Fouque K, Lavanant H, Zirah S, Hegemann JD, Fage CD, Marahiel MA, Rebuffat S, Afonso C Analyst. 2018 Feb 6. doi: 10.1039/c7an02052j. PMID:29404537<ref>PMID:29404537</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5oqz" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Rubgi]]
	[[Category: Fage, C D]]		[[Category: Fage, C D]]
	[[Category: Hegemann, J D]]		[[Category: Hegemann, J D]]

OCA at 06:11, 7 February 2018

OCA — Wed, 07 Feb 2018 06:11:52 GMT

←Older revision		Revision as of 06:11, 7 February 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5oqz ~~is ON HOLD~~	+	==Crystal structure of the lasso peptide rubrivinodin==
-		+	<StructureSection load='5oqz' size='340' side='right' caption='[[5oqz]], [[Resolution\|resolution]] 0.81Å' scene=''>
-	~~Authors~~: ~~Fage~~, C.D., ~~Hegemann~~, J.D., ~~Marahiel~~, M.A.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5oqz]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OQZ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OQZ FirstGlance]. <br>
-	~~Description: Crystal structure of the lasso peptide rubrivinodin~~	+	</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=5oqz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5oqz OCA], [http://pdbe.org/5oqz PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5oqz RCSB], [http://www.ebi.ac.uk/pdbsum/5oqz PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5oqz ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
-	[[Category: Hegemann, J.D]]	+	__TOC__
-	[[Category: Marahiel, M.A]]	+	</StructureSection>
-	[[Category: ~~Fage, C.D~~]]	+	[[Category: Fage, C D]]
		+	[[Category: Hegemann, J D]]
		+	[[Category: Marahiel, M A]]
		+	[[Category: Lasso peptide]]
		+	[[Category: Ribosomally synthesized and post-translationally modified peptide]]
		+	[[Category: Ripp]]
		+	[[Category: Unknown function]]

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

OCA — Wed, 27 Sep 2017 12:44:34 GMT

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

←Older revision

Revision as of 12:44, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5oqz is ON HOLD Authors: Fage, C.D., Hegemann, J.D., Marahiel, M.A. Description: Crystal structure of the lasso peptide rubrivinodin [[Category: Un...

OCA — Wed, 27 Sep 2017 12:44:32 GMT

New page: '''Unreleased structure''' The entry 5oqz is ON HOLD Authors: Fage, C.D., Hegemann, J.D., Marahiel, M.A. Description: Crystal structure of the lasso peptide rubrivinodin [[Category: Un...

New page

'''Unreleased structure'''

The entry 5oqz is ON HOLD

Authors: Fage, C.D., Hegemann, J.D., Marahiel, M.A.

Description: Crystal structure of the lasso peptide rubrivinodin
[[Category: Unreleased Structures]]
[[Category: Hegemann, J.D]]
[[Category: Marahiel, M.A]]
[[Category: Fage, C.D]]