5yed - Revision history

OCA at 10:23, 27 March 2024

OCA — Wed, 27 Mar 2024 10:23:07 GMT

←Older revision		Revision as of 10:23, 27 March 2024
Line 1:		Line 1:

	==Crystal structure of LokiProfilin1==		==Crystal structure of LokiProfilin1==
-	<StructureSection load='5yed' size='340' side='right' caption='[[5yed]], [[Resolution\|resolution]] 1.60Å' scene=''>	+	<StructureSection load='5yed' size='340' side='right'caption='[[5yed]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yed]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Lokiarchaeum_sp.~~_gc14_75~~ Lokiarchaeum sp. ~~gc14_75~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YED OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5YED FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yed]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Lokiarchaeum_sp._GC14_75 Lokiarchaeum sp. GC14_75]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YED OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YED FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~Lokiarch_47830 (~~[~~http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=1538547 Lokiarchaeum sp. GC14_75])~~</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]] 1.6Å</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=5yed FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yed OCA], [~~http~~://pdbe.org/5yed PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5yed RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5yed PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5yed 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=5yed FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yed OCA], [https://pdbe.org/5yed PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5yed RCSB], [https://www.ebi.ac.uk/pdbsum/5yed PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5yed ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/PROF1_LOKSG PROF1_LOKSG] Binds to actin and affects the structure of the cytoskeleton. At high concentrations inhibits spontaneous rabbit actin nucleation. This strongly suggests this archaea has a profilin-regulated actin system, and actin-type genes can be identified in this organism.<ref>PMID:30283132</ref>
-	~~The origin of the eukaryotic cell is unresolved(1,2)~~. Metagenomics sequencing has recently identified several potential eukaryotic gene homologues in Asgard archaea(3,4), consistent with the hypothesis that the eukaryotic cell evolved from within the Archaea domain. ~~However, many of these eukaryotic-like sequences are highly divergent and the organisms have yet~~ to be imaged or cultivated, which brings into question the extent to which these archaeal proteins represent functional equivalents of their eukaryotic counterparts. Here we show that Asgard archaea encode functional profilins and ~~thereby establish that this archaeal superphylum has a regulated actin cytoskeleton, one of~~ the ~~hallmarks~~ of the ~~eukaryotic cell(5)~~. ~~Loki profilin-1, Loki profilin-2 and Odin profilin adopt the typical profilin fold and are able to interact with~~ rabbit actin-an interaction that involves proteins from species that diverged more than 1.2 billion years ago(6). Biochemical experiments reveal that mammalian actin polymerizes in the presence of Asgard profilins; however, Loki, Odin and Heimdall profilins impede pointed-end elongation. These archaeal profilins also retard the spontaneous nucleation ~~of actin filaments, an effect that is reduced in the presence of phospholipids~~. ~~Asgard profilins do not interact with polyproline motifs and the profilin-polyproline interaction therefore probably evolved later in the Eukarya lineage. These results suggest that Asgard~~ archaea ~~possess~~ a ~~primordial, polar,~~ profilin-regulated actin system, ~~which may be localized to membranes owing to the sensitivity of Asgard profilins to phospholipids. Because Asgard archaea are also predicted to encode potential eukaryotic~~-~~like~~ genes ~~involved~~ in membrane-trafficking and endocytosis(3,4), imaging is now necessary to elucidate whether these organisms are capable of generating eukaryotic-like membrane dynamics that are regulated by actin, such as are observed in eukaryotic cell movement, podosomes and endocytosis.	+
-		+
-	~~Genomes of Asgard archaea encode profilins that regulate actin.,Akil C, Robinson RC Nature. 2018 Oct 3. pii: 10.1038/s41586-018-0548-6. doi:, 10.1038/s41586-018-0548-6. PMID:30283132~~<ref>PMID:30283132</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 5yed" style="background-color:#fffaf0;"></div~~>	+
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Lokiarchaeum sp. gc14_75~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Akil, C~~]]	+	[[Category: Lokiarchaeum sp. GC14_75]]
-	[[Category: ~~Robinson, R~~ C]]	+	[[Category: Akil C]]
-	[[Category: ~~Actin]]~~	+	[[Category: Robinson RC]]
-	~~[[Category: Archaea]]~~	+
-	~~[[Category: Structural protein~~]]	+

OCA at 08:30, 17 October 2018

OCA — Wed, 17 Oct 2018 08:30:01 GMT

←Older revision		Revision as of 08:30, 17 October 2018
Line 7:		Line 7:
	<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=5yed FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yed OCA], [http://pdbe.org/5yed PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yed RCSB], [http://www.ebi.ac.uk/pdbsum/5yed PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yed 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=5yed FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yed OCA], [http://pdbe.org/5yed PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yed RCSB], [http://www.ebi.ac.uk/pdbsum/5yed PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yed ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The origin of the eukaryotic cell is unresolved(1,2). Metagenomics sequencing has recently identified several potential eukaryotic gene homologues in Asgard archaea(3,4), consistent with the hypothesis that the eukaryotic cell evolved from within the Archaea domain. However, many of these eukaryotic-like sequences are highly divergent and the organisms have yet to be imaged or cultivated, which brings into question the extent to which these archaeal proteins represent functional equivalents of their eukaryotic counterparts. Here we show that Asgard archaea encode functional profilins and thereby establish that this archaeal superphylum has a regulated actin cytoskeleton, one of the hallmarks of the eukaryotic cell(5). Loki profilin-1, Loki profilin-2 and Odin profilin adopt the typical profilin fold and are able to interact with rabbit actin-an interaction that involves proteins from species that diverged more than 1.2 billion years ago(6). Biochemical experiments reveal that mammalian actin polymerizes in the presence of Asgard profilins; however, Loki, Odin and Heimdall profilins impede pointed-end elongation. These archaeal profilins also retard the spontaneous nucleation of actin filaments, an effect that is reduced in the presence of phospholipids. Asgard profilins do not interact with polyproline motifs and the profilin-polyproline interaction therefore probably evolved later in the Eukarya lineage. These results suggest that Asgard archaea possess a primordial, polar, profilin-regulated actin system, which may be localized to membranes owing to the sensitivity of Asgard profilins to phospholipids. Because Asgard archaea are also predicted to encode potential eukaryotic-like genes involved in membrane-trafficking and endocytosis(3,4), imaging is now necessary to elucidate whether these organisms are capable of generating eukaryotic-like membrane dynamics that are regulated by actin, such as are observed in eukaryotic cell movement, podosomes and endocytosis.
		+
		+	Genomes of Asgard archaea encode profilins that regulate actin.,Akil C, Robinson RC Nature. 2018 Oct 3. pii: 10.1038/s41586-018-0548-6. doi:, 10.1038/s41586-018-0548-6. PMID:30283132<ref>PMID:30283132</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5yed" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 08:25, 10 October 2018

OCA — Wed, 10 Oct 2018 08:25:31 GMT

←Older revision		Revision as of 08:25, 10 October 2018
Line 3:		Line 3:
	<StructureSection load='5yed' size='340' side='right' caption='[[5yed]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='5yed' size='340' side='right' caption='[[5yed]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yed]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YED OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YED FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yed]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Lokiarchaeum_sp._gc14_75 Lokiarchaeum sp. gc14_75]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YED OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YED 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=5yed FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yed OCA], [http://pdbe.org/5yed PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yed RCSB], [http://www.ebi.ac.uk/pdbsum/5yed PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yed ProSAT]</span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Lokiarch_47830 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1538547 Lokiarchaeum sp. GC14_75])</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=5yed FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yed OCA], [http://pdbe.org/5yed PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yed RCSB], [http://www.ebi.ac.uk/pdbsum/5yed PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yed ProSAT]</span></td></tr>
	</table>		</table>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Lokiarchaeum sp. gc14_75]]
	[[Category: Akil, C]]		[[Category: Akil, C]]
	[[Category: Robinson, R C]]		[[Category: Robinson, R C]]

OCA at 19:38, 19 September 2018

OCA — Wed, 19 Sep 2018 19:38:29 GMT

←Older revision		Revision as of 19:38, 19 September 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5yed is ~~ON HOLD until Paper Publication~~	+	==Crystal structure of LokiProfilin1==
-		+	<StructureSection load='5yed' size='340' side='right' caption='[[5yed]], [[Resolution\|resolution]] 1.60Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5yed]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YED OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YED FirstGlance]. <br>
-	~~Description~~:	+	</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=5yed FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yed OCA], [http://pdbe.org/5yed PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yed RCSB], [http://www.ebi.ac.uk/pdbsum/5yed PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yed ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Akil, C]]
		+	[[Category: Robinson, R C]]
		+	[[Category: Actin]]
		+	[[Category: Archaea]]
		+	[[Category: Structural protein]]

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

OCA — Wed, 27 Sep 2017 16:28:20 GMT

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

←Older revision

Revision as of 16:28, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5yed is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Wed, 27 Sep 2017 16:28:19 GMT

New page: '''Unreleased structure''' The entry 5yed is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5yed is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]