4gc5 - Revision history

OCA at 06:47, 26 October 2022

OCA — Wed, 26 Oct 2022 06:47:23 GMT

←Older revision		Revision as of 06:47, 26 October 2022
Line 1:		Line 1:

	==Crystal structure of murine TFB1M==		==Crystal structure of murine TFB1M==
-	<StructureSection load='4gc5' size='340' side='right' caption='[[4gc5]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<StructureSection load='4gc5' size='340' side='right'caption='[[4gc5]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4gc5]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Lk3_transgenic_mice Lk3 transgenic mice~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GC5 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4GC5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4gc5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GC5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4GC5 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=4gc5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gc5 OCA], [https://pdbe.org/4gc5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4gc5 RCSB], [https://www.ebi.ac.uk/pdbsum/4gc5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4gc5 ProSAT]</span></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4gc9\|4gc9]]</td></tr>~~	+
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Tfb1m ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])~~</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=4gc5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gc5 OCA], [~~http~~://pdbe.org/4gc5 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4gc5 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4gc5 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4gc5 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/TFB1M_MOUSE TFB1M_MOUSE]] S-adenosyl-L-methionine-dependent methyltransferase which specifically dimethylates mitochondrial 12S rRNA at the conserved stem loop. Also required for basal transcription of mitochondrial DNA, probably via its interaction with POLRMT and TFAM. Stimulates transcription independently of the methyltransferase activity (By similarity).	+	[https://www.uniprot.org/uniprot/TFB1M_MOUSE TFB1M_MOUSE] S-adenosyl-L-methionine-dependent methyltransferase which specifically dimethylates mitochondrial 12S rRNA at the conserved stem loop. Also required for basal transcription of mitochondrial DNA, probably via its interaction with POLRMT and TFAM. Stimulates transcription independently of the methyltransferase activity (By similarity).
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 25:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Lk3 transgenic mice~~]]	+	[[Category: Large Structures]]
-	[[Category: Garcia-Diaz, M]]	+	[[Category: Mus musculus]]
-	[[Category: Guja~~, K E~~]]	+	[[Category: Garcia-Diaz M]]
-	[[Category: Hambardjieva, E]]	+	[[Category: Guja KE]]
-	[[Category: Karzai~~, A W~~]]	+	[[Category: Hambardjieva E]]
-	[[Category: Mejia, E]]	+	[[Category: Karzai AW]]
-	[[Category: Shi, H]]	+	[[Category: Mejia E]]
-	[[Category: Venkataraman, K]]	+	[[Category: Shi H]]
-	[[Category: Yakubovskaya, E]]	+	[[Category: Venkataraman K]]
-	~~[[Category: Methylation]]~~	+	[[Category: Yakubovskaya E]]
-	~~[[Category: Methyltransferase fold]]~~	+
-	~~[[Category: Mitochondria]]~~	+
-	~~[[Category: Rrna methyltransferase]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 01:34, 5 August 2016

OCA — Fri, 05 Aug 2016 01:34:27 GMT

←Older revision		Revision as of 01:34, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of murine TFB1M==		==Crystal structure of murine TFB1M==
	<StructureSection load='4gc5' size='340' side='right' caption='[[4gc5]], [[Resolution\|resolution]] 1.80Å' scene=''>		<StructureSection load='4gc5' size='340' side='right' caption='[[4gc5]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4gc5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Mus_musculus Mus musculus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GC5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4GC5 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4gc5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GC5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4GC5 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4gc9\|4gc9]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4gc9\|4gc9]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Tfb1m ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 ~~Mus musculus~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Tfb1m ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 LK3 transgenic mice])</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=4gc5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gc5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4gc5 RCSB], [http://www.ebi.ac.uk/pdbsum/4gc5 PDBsum]</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=4gc5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gc5 OCA], [http://pdbe.org/4gc5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4gc5 RCSB], [http://www.ebi.ac.uk/pdbsum/4gc5 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4gc5 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 4gc5" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Mus musculus~~]]	+	[[Category: Lk3 transgenic mice]]
	[[Category: Garcia-Diaz, M]]		[[Category: Garcia-Diaz, M]]
	[[Category: Guja, K E]]		[[Category: Guja, K E]]

OCA at 21:38, 24 December 2014

OCA — Wed, 24 Dec 2014 21:38:55 GMT

←Older revision		Revision as of 21:38, 24 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_4gc5\| PDB~~=4gc5 \| ~~SCENE~~= }}	+	==Crystal structure of murine TFB1M==
-	===~~Crystal~~ structure ~~of murine TFB1M~~===	+	<StructureSection load='4gc5' size='340' side='right' caption='[[4gc5]], [[Resolution\|resolution]] 1.80Å' scene=''>
-	~~{{ABSTRACT_PUBMED_23804760}}~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4gc5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GC5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4GC5 FirstGlance]. <br>
-	==Function==	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[4gc9\|4gc9]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Tfb1m ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10090 Mus musculus])</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=4gc5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gc5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4gc5 RCSB], [http://www.ebi.ac.uk/pdbsum/4gc5 PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
	[[http://www.uniprot.org/uniprot/TFB1M_MOUSE TFB1M_MOUSE]] S-adenosyl-L-methionine-dependent methyltransferase which specifically dimethylates mitochondrial 12S rRNA at the conserved stem loop. Also required for basal transcription of mitochondrial DNA, probably via its interaction with POLRMT and TFAM. Stimulates transcription independently of the methyltransferase activity (By similarity).		[[http://www.uniprot.org/uniprot/TFB1M_MOUSE TFB1M_MOUSE]] S-adenosyl-L-methionine-dependent methyltransferase which specifically dimethylates mitochondrial 12S rRNA at the conserved stem loop. Also required for basal transcription of mitochondrial DNA, probably via its interaction with POLRMT and TFAM. Stimulates transcription independently of the methyltransferase activity (By similarity).
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Eukaryotic transcription factor B (TFB) proteins are homologous to KsgA/Dim1 ribosomal RNA (rRNA) methyltransferases. The mammalian TFB1, mitochondrial (TFB1M) factor is an essential protein necessary for mitochondrial gene expression. TFB1M mediates an rRNA modification in the small ribosomal subunit and thus plays a role analogous to KsgA/Dim1 proteins. This modification has been linked to mitochondrial dysfunctions leading to maternally inherited deafness, aminoglycoside sensitivity and diabetes. Here, we present the first structural characterization of the mammalian TFB1 factor. We have solved two X-ray crystallographic structures of TFB1M with (2.1 A) and without (2.0 A) its cofactor S-adenosyl-L-methionine. These structures reveal that TFB1M shares a conserved methyltransferase core with other KsgA/Dim1 methyltransferases and shed light on the structural basis of S-adenosyl-L-methionine binding and methyltransferase activity. Together with mutagenesis studies, these data suggest a model for substrate binding and provide insight into the mechanism of methyl transfer, clarifying the role of this factor in an essential process for mitochondrial function.

-	~~==About this Structure==~~	+	Structural basis for S-adenosylmethionine binding and methyltransferase activity by mitochondrial transcription factor B1.,Guja KE, Venkataraman K, Yakubovskaya E, Shi H, Mejia E, Hambardjieva E, Karzai AW, Garcia-Diaz M Nucleic Acids Res. 2013 Jun 26. PMID:23804760<ref>PMID:23804760</ref>
-	~~[[4gc5]] is a 1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Mus_musculus Mus musculus]~~. ~~Full crystallographic information is available from [http~~:/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=4GC5 OCA].~~	+

-	==~~Reference~~==	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~<ref group="xtra">PMID:023804760</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	</div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Mus musculus]]		[[Category: Mus musculus]]
-	[[Category: Garcia-Diaz, M.]]	+	[[Category: Garcia-Diaz, M]]
-	[[Category: Guja, K E.]]	+	[[Category: Guja, K E]]
-	[[Category: Hambardjieva, E.]]	+	[[Category: Hambardjieva, E]]
-	[[Category: Karzai, A W.]]	+	[[Category: Karzai, A W]]
-	[[Category: Mejia, E.]]	+	[[Category: Mejia, E]]
-	[[Category: Shi, H.]]	+	[[Category: Shi, H]]
-	[[Category: Venkataraman, K.]]	+	[[Category: Venkataraman, K]]
-	[[Category: Yakubovskaya, E.]]	+	[[Category: Yakubovskaya, E]]
	[[Category: Methylation]]		[[Category: Methylation]]
	[[Category: Methyltransferase fold]]		[[Category: Methyltransferase fold]]

OCA at 15:36, 10 July 2013

OCA — Wed, 10 Jul 2013 15:36:43 GMT

←Older revision		Revision as of 15:36, 10 July 2013
Line 1:		Line 1:
-	~~'''Unreleased~~ structure~~'''~~	+	{{STRUCTURE_4gc5\| PDB=4gc5 \| SCENE= }}
		+	===Crystal structure of murine TFB1M===
		+	{{ABSTRACT_PUBMED_23804760}}

-	~~The entry 4gc5 is ON HOLD until Paper Publication~~	+	==Function==
		+	[[http://www.uniprot.org/uniprot/TFB1M_MOUSE TFB1M_MOUSE]] S-adenosyl-L-methionine-dependent methyltransferase which specifically dimethylates mitochondrial 12S rRNA at the conserved stem loop. Also required for basal transcription of mitochondrial DNA, probably via its interaction with POLRMT and TFAM. Stimulates transcription independently of the methyltransferase activity (By similarity).

-	~~Authors~~: ~~Guja, K~~.E.~~, Yakubovskaya, E~~.~~, Shi, H., Mejia, E., Hambardjieva, E., Venkataraman, K~~.~~, Karzai, A~~.W.~~, Garcia~~-~~Diaz, M~~.	+	==About this Structure==
		+	[[4gc5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GC5 OCA].

-	~~Description~~: ~~Crystal structure of murine TFB1M~~	+	==Reference==
		+	<ref group="xtra">PMID:023804760</ref><references group="xtra"/><references/>
		+	[[Category: Mus musculus]]
		+	[[Category: Garcia-Diaz, M.]]
		+	[[Category: Guja, K E.]]
		+	[[Category: Hambardjieva, E.]]
		+	[[Category: Karzai, A W.]]
		+	[[Category: Mejia, E.]]
		+	[[Category: Shi, H.]]
		+	[[Category: Venkataraman, K.]]
		+	[[Category: Yakubovskaya, E.]]
		+	[[Category: Methylation]]
		+	[[Category: Methyltransferase fold]]
		+	[[Category: Mitochondria]]
		+	[[Category: Rrna methyltransferase]]
		+	[[Category: Transferase]]

OCA at 04:50, 12 September 2012

OCA — Wed, 12 Sep 2012 04:50:05 GMT

←Older revision		Revision as of 04:50, 12 September 2012
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4gc5 is ON HOLD	+	The entry 4gc5 is ON HOLD until Paper Publication

	Authors: Guja, K.E., Yakubovskaya, E., Shi, H., Mejia, E., Hambardjieva, E., Venkataraman, K., Karzai, A.W., Garcia-Diaz, M.		Authors: Guja, K.E., Yakubovskaya, E., Shi, H., Mejia, E., Hambardjieva, E., Venkataraman, K., Karzai, A.W., Garcia-Diaz, M.

	Description: Crystal structure of murine TFB1M		Description: Crystal structure of murine TFB1M

OCA: Protected "4gc5" [edit=sysop:move=sysop]

OCA — Wed, 08 Aug 2012 05:00:02 GMT

Protected "4gc5" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:00, 8 August 2012

OCA: New page: '''Unreleased structure''' The entry 4gc5 is ON HOLD Authors: Guja, K.E., Yakubovskaya, E., Shi, H., Mejia, E., Hambardjieva, E., Venkataraman, K., Karzai, A.W., Garcia-Diaz, M. Descri...

OCA — Wed, 08 Aug 2012 05:00:01 GMT

New page: '''Unreleased structure''' The entry 4gc5 is ON HOLD Authors: Guja, K.E., Yakubovskaya, E., Shi, H., Mejia, E., Hambardjieva, E., Venkataraman, K., Karzai, A.W., Garcia-Diaz, M. Descri...

New page

'''Unreleased structure'''

The entry 4gc5 is ON HOLD

Authors: Guja, K.E., Yakubovskaya, E., Shi, H., Mejia, E., Hambardjieva, E., Venkataraman, K., Karzai, A.W., Garcia-Diaz, M.

Description: Crystal structure of murine TFB1M