7bte - Revision history

OCA at 10:49, 27 March 2024

OCA — Wed, 27 Mar 2024 10:49:13 GMT

←Older revision		Revision as of 10:49, 27 March 2024
Line 3:		Line 3:
	<StructureSection load='7bte' size='340' side='right'caption='[[7bte]], [[Resolution\|resolution]] 4.20Å' scene=''>		<StructureSection load='7bte' size='340' side='right'caption='[[7bte]], [[Resolution\|resolution]] 4.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7bte]] is a 8 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7BTE OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=7BTE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7bte]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus] and [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7BTE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7BTE FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution\|Resolution]] 4.2Å</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=7bte FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7bte OCA], [~~http~~://pdbe.org/7bte PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=7bte RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/7bte PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=7bte ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=7bte FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7bte OCA], [https://pdbe.org/7bte PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7bte RCSB], [https://www.ebi.ac.uk/pdbsum/7bte PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7bte ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~ACTS_CHICK ACTS_CHICK~~]~~] Actins are highly conserved proteins~~ that ~~are involved in various types of cell motility and are ubiquitously expressed in all eukaryotic cells.~~	+	[https://www.uniprot.org/uniprot/AB140_YEAST AB140_YEAST] S-adenosyl-L-methionine-dependent methyltransferase that mediates N(3)-methylcytidine modification of residue 32 of the tRNA anticodon loop of tRNA(Thr) and tRNA(Ser) (PubMed:21518804, PubMed:21518805, PubMed:28003514). N(3)-methylcytidine methylation of tRNA(Thr) requires the N6-threonylcarbamoylation of tRNA (t6A37) by the EKC/KEOPS complex as prerequisite (PubMed:28003514). N(3)-methylcytidine methylation of tRNA(Ser) requires the formation of N(6)-dimethylallyladenosine(37) (i6A37) by MOD5 as prerequisite (PubMed:28003514). Methylation of tRNA(Ser) is also stimulated by SES1 (PubMed:28003514). Binds F-actin and shows weak F-actin cross-linking activity (PubMed:9467951).<ref>PMID:21518804</ref> <ref>PMID:21518805</ref> <ref>PMID:28003514</ref> <ref>PMID:9467951</ref>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	~~Cellular studies of filamentous actin~~ (F-~~actin) processes commonly utilize fluorescent versions~~ of ~~toxins, peptides, and proteins that bind actin. While the choice~~ of these markers has been largely based on availability and ease, there is a severe dearth of structural data for an informed judgment in employing suitable F-actin markers for a particular requirement. Here, we describe the ~~electron cryomicroscopy structures~~ of ~~phalloidin, lifeAct,~~ and ~~utrophin bound to F-actin~~, providing a comprehensive high-resolution structural comparison of widely used actin markers and their influence towards F-actin. Our results show that phalloidin binding does not induce specific conformational change and lifeAct specifically recognizes closed D-loop conformation, i.~~e., ADP~~-~~Pi or ADP states~~ of F-~~actin. The structural models aided designing~~ of ~~minimal utrophin and a shorter lifeAct, which can be utilized~~ as ~~F-actin marker~~. ~~Together, our study provides a structural perspective, where~~ the ~~binding sites~~ of ~~utrophin and lifeAct overlap with majority of actin~~-~~binding proteins and thus offering an invaluable resource for researchers in choosing appropriate actin markers and generating new marker variants.~~	+
-		+
-	~~Structural insights into actin filament recognition~~ by ~~commonly used cellular actin markers~~.~~,Kumari A, Kesarwani S, Javoor MG, Vinothkumar KR, Sirajuddin M EMBO J. 2020 Jul 15;39~~(14):~~e104006~~. ~~doi~~: ~~10.15252/embj.2019104006. Epub 2020 Jun , 22~~. PMID:~~32567727~~<ref>PMID:~~32567727~~</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.~~<br>	+
-	</~~div~~>	+
-	<~~div class="pdbe-citations 7bte" style="background-color:#fffaf0;"~~></~~div~~>	+

	==See Also==		==See Also==
Line 27:		Line 19:
	[[Category: Gallus gallus]]		[[Category: Gallus gallus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Kumari, A~~]]	+	[[Category: Saccharomyces cerevisiae]]
-	[[Category: ~~Ragunath, V K~~]]	+	[[Category: Kumari A]]
-	[[Category: ~~Sirajuddin, M~~]]	+	[[Category: Ragunath VK]]
-	[[Category: ~~Adp-f-actin]]~~	+	[[Category: Sirajuddin M]]
-	~~[[Category: Contractile protein-protein binding complex]]~~	+
-	~~[[Category: F-actin~~]]	+

OCA at 11:49, 22 July 2020

OCA — Wed, 22 Jul 2020 11:49:47 GMT

←Older revision		Revision as of 11:49, 22 July 2020
Line 1:		Line 1:

	==Lifeact-F-actin complex==		==Lifeact-F-actin complex==
-	<StructureSection load='7bte' size='340' side='right'caption='[[7bte]]' scene=''>	+	<StructureSection load='7bte' size='340' side='right'caption='[[7bte]], [[Resolution\|resolution]] 4.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7BTE OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7BTE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7bte]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7BTE OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7BTE FirstGlance]. <br>
-	</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=7bte FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7bte OCA], [http://pdbe.org/7bte PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7bte RCSB], [http://www.ebi.ac.uk/pdbsum/7bte PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7bte ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></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=7bte FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7bte OCA], [http://pdbe.org/7bte PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7bte RCSB], [http://www.ebi.ac.uk/pdbsum/7bte PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7bte ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/ACTS_CHICK ACTS_CHICK]] Actins are highly conserved proteins that are involved in various types of cell motility and are ubiquitously expressed in all eukaryotic cells.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Cellular studies of filamentous actin (F-actin) processes commonly utilize fluorescent versions of toxins, peptides, and proteins that bind actin. While the choice of these markers has been largely based on availability and ease, there is a severe dearth of structural data for an informed judgment in employing suitable F-actin markers for a particular requirement. Here, we describe the electron cryomicroscopy structures of phalloidin, lifeAct, and utrophin bound to F-actin, providing a comprehensive high-resolution structural comparison of widely used actin markers and their influence towards F-actin. Our results show that phalloidin binding does not induce specific conformational change and lifeAct specifically recognizes closed D-loop conformation, i.e., ADP-Pi or ADP states of F-actin. The structural models aided designing of minimal utrophin and a shorter lifeAct, which can be utilized as F-actin marker. Together, our study provides a structural perspective, where the binding sites of utrophin and lifeAct overlap with majority of actin-binding proteins and thus offering an invaluable resource for researchers in choosing appropriate actin markers and generating new marker variants.
		+
		+	Structural insights into actin filament recognition by commonly used cellular actin markers.,Kumari A, Kesarwani S, Javoor MG, Vinothkumar KR, Sirajuddin M EMBO J. 2020 Jul 15;39(14):e104006. doi: 10.15252/embj.2019104006. Epub 2020 Jun , 22. PMID:32567727<ref>PMID:32567727</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7bte" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Actin 3D structures\|Actin 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Gallus gallus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Kumari A]]	+	[[Category: Kumari, A]]
-	[[Category: Ragunath VK]]	+	[[Category: Ragunath, V K]]
-	[[Category: Sirajuddin M]]	+	[[Category: Sirajuddin, M]]
		+	[[Category: Adp-f-actin]]
		+	[[Category: Contractile protein-protein binding complex]]
		+	[[Category: F-actin]]

OCA at 05:53, 20 May 2020

OCA — Wed, 20 May 2020 05:53:40 GMT

←Older revision		Revision as of 05:53, 20 May 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 7bte ~~is ON HOLD until Apr 01 2022~~	+	==Lifeact-F-actin complex==
-		+	<StructureSection load='7bte' size='340' side='right'caption='[[7bte]]' scene=''>
-	~~Authors~~: ~~Kumari~~, A., ~~Ragunath~~, V.K., ~~Sirajuddin~~, M.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7BTE OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7BTE FirstGlance]. <br>
-	~~Description: Lifeact-F-actin complex~~	+	</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=7bte FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7bte OCA], [http://pdbe.org/7bte PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7bte RCSB], [http://www.ebi.ac.uk/pdbsum/7bte PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7bte ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: Kumari, A]]	+	__TOC__
-	[[Category: Ragunath~~, V.K~~]]	+	</StructureSection>
-	[[Category: Sirajuddin, M]]	+	[[Category: Large Structures]]
		+	[[Category: Kumari A]]
		+	[[Category: Ragunath VK]]
		+	[[Category: Sirajuddin M]]

OCA at 05:41, 15 April 2020

OCA — Wed, 15 Apr 2020 05:41:09 GMT

←Older revision		Revision as of 05:41, 15 April 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7bte is ON HOLD	+	The entry 7bte is ON HOLD until Apr 01 2022

	Authors: Kumari, A., Ragunath, V.K., Sirajuddin, M.		Authors: Kumari, A., Ragunath, V.K., Sirajuddin, M.

OCA: Protected "7bte" [edit=sysop:move=sysop]

OCA — Wed, 08 Apr 2020 05:52:48 GMT

Protected "7bte" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:52, 8 April 2020

OCA: New page: '''Unreleased structure''' The entry 7bte is ON HOLD Authors: Kumari, A., Ragunath, V.K., Sirajuddin, M. Description: Lifeact-F-actin complex Category: Unreleased Structures [[Cate...

OCA — Wed, 08 Apr 2020 05:52:46 GMT

New page: '''Unreleased structure''' The entry 7bte is ON HOLD Authors: Kumari, A., Ragunath, V.K., Sirajuddin, M. Description: Lifeact-F-actin complex Category: Unreleased Structures [[Cate...

New page

'''Unreleased structure'''

The entry 7bte is ON HOLD

Authors: Kumari, A., Ragunath, V.K., Sirajuddin, M.

Description: Lifeact-F-actin complex
[[Category: Unreleased Structures]]
[[Category: Kumari, A]]
[[Category: Ragunath, V.K]]
[[Category: Sirajuddin, M]]