6w6f - Revision history

OCA at 14:17, 18 October 2023

OCA — Wed, 18 Oct 2023 14:17:41 GMT

←Older revision		Revision as of 14:17, 18 October 2023
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	<StructureSection load='6w6f' size='340' side='right'caption='[[6w6f]], [[Resolution\|resolution]] 3.20Å' scene=''>		<StructureSection load='6w6f' size='340' side='right'caption='[[6w6f]], [[Resolution\|resolution]] 3.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6w6f]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6W6F OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6W6F FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6w6f]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6W6F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6W6F FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[6w6c\|6w6c]]</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]] 3.2Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">DIMT1, DIMT1L, HUSSY-05 ([http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=9606 HUMAN])</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=6w6f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6w6f OCA], [https://pdbe.org/6w6f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6w6f RCSB], [https://www.ebi.ac.uk/pdbsum/6w6f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6w6f ProSAT]</span></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/18S_rRNA_(adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase 18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.183 2.1.1.183] </span></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=6w6f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6w6f OCA], [~~http~~://pdbe.org/6w6f PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6w6f RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6w6f PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6w6f ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/DIM1_HUMAN DIM1_HUMAN]] Specifically dimethylates two adjacent adenosines in the loop of a conserved hairpin near the 3'-end of 18S rRNA in the 40S particle (PubMed:25851604). Involved in the pre-rRNA processing steps leading to small-subunit rRNA production independently of its RNA-modifying catalytic activity (PubMed:25851604).<ref>PMID:25851604</ref>	+	[https://www.uniprot.org/uniprot/DIM1_HUMAN DIM1_HUMAN] Specifically dimethylates two adjacent adenosines in the loop of a conserved hairpin near the 3'-end of 18S rRNA in the 40S particle (PubMed:25851604). Involved in the pre-rRNA processing steps leading to small-subunit rRNA production independently of its RNA-modifying catalytic activity (PubMed:25851604).<ref>PMID:25851604</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Shen, H]]	+	[[Category: Shen H]]
-	[[Category: Stoute, J]]	+	[[Category: Stoute J]]
-	~~[[Category: Rna binding protein]]~~	+
-	~~[[Category: Rna modification enzyme~~]]	+

OCA at 07:08, 2 September 2020

OCA — Wed, 02 Sep 2020 07:08:28 GMT

←Older revision		Revision as of 07:08, 2 September 2020
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	==Structural and catalytic roles of human 18S rRNA methyltransferases DIMT1 in ribosome assembly and translation==		==Structural and catalytic roles of human 18S rRNA methyltransferases DIMT1 in ribosome assembly and translation==
-	<StructureSection load='6w6f' size='340' side='right'caption='[[6w6f]]' scene=''>	+	<StructureSection load='6w6f' size='340' side='right'caption='[[6w6f]], [[Resolution\|resolution]] 3.20Å' 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=6W6F OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6W6F FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6w6f]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6W6F OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6W6F 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=6w6f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6w6f OCA], [http://pdbe.org/6w6f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6w6f RCSB], [http://www.ebi.ac.uk/pdbsum/6w6f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6w6f ProSAT]</span></td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6w6c\|6w6c]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">DIMT1, DIMT1L, HUSSY-05 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/18S_rRNA_(adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase 18S rRNA (adenine(1779)-N(6)/adenine(1780)-N(6))-dimethyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.183 2.1.1.183] </span></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=6w6f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6w6f OCA], [http://pdbe.org/6w6f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6w6f RCSB], [http://www.ebi.ac.uk/pdbsum/6w6f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6w6f ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DIM1_HUMAN DIM1_HUMAN]] Specifically dimethylates two adjacent adenosines in the loop of a conserved hairpin near the 3'-end of 18S rRNA in the 40S particle (PubMed:25851604). Involved in the pre-rRNA processing steps leading to small-subunit rRNA production independently of its RNA-modifying catalytic activity (PubMed:25851604).<ref>PMID:25851604</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	rRNA-modifying enzymes participate in ribosome assembly. However, whether the catalytic activities of these enzymes are important for the ribosome assembly and other cellular processes is not fully understood. Here, we report the crystal structure of WT human dimethyladenosine transferase 1 (DIMT1), an 18S rRNA N (6,6)-dimethyladenosine (m2 (6,6)A) methyltransferase, and results obtained with a catalytically inactive DIMT1 variant. We found that DIMT1 (+/-) heterozygous HEK 293T cells have a significantly decreased 40S fraction and reduced protein synthesis but no major changes in m2 (6,6)A levels in 18S rRNA. Expression of a catalytically inactive variant, DIMT1-E85A, in WT and DIMT1 (+/-) cells significantly decreased m2 (6,6)A levels in 18S rRNA, indicating a dominant-negative effect of this variant on m2 (6,6)A levels. However, expression of the DIMT1-E85A variant restored the defects in 40S levels. Of note, unlike WT DIMT1, DIMT1-E85A could not revert the defects in protein translation. We found that the differences between this variant and the WT enzyme extended to translation fidelity and gene expression patterns in DNA damage response pathways. These results suggest that the catalytic activity of DIMT1 is involved in protein translation and that the overall protein scaffold of DIMT1, regardless of the catalytic activity on m2 (6,6)A in 18S rRNA, is essential for 40S assembly.
		+
		+	Structural and catalytic roles of the human 18S rRNA methyltransferases DIMT1 in ribosome assembly and translation.,Shen H, Stoute J, Liu KF J Biol Chem. 2020 Aug 21;295(34):12058-12070. doi: 10.1074/jbc.RA120.014236. Epub, 2020 Jul 2. PMID:32616653<ref>PMID:32616653</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6w6f" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Shen H]]	+	[[Category: Shen, H]]
-	[[Category: Stoute J]]	+	[[Category: Stoute, J]]
		+	[[Category: Rna binding protein]]
		+	[[Category: Rna modification enzyme]]

OCA at 14:08, 8 July 2020

OCA — Wed, 08 Jul 2020 14:08:04 GMT

←Older revision		Revision as of 14:08, 8 July 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 6w6f ~~is ON HOLD until Paper Publication~~	+	==Structural and catalytic roles of human 18S rRNA methyltransferases DIMT1 in ribosome assembly and translation==
-		+	<StructureSection load='6w6f' size='340' side='right'caption='[[6w6f]]' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6W6F OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6W6F FirstGlance]. <br>
-	~~Description~~:	+	</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=6w6f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6w6f OCA], [http://pdbe.org/6w6f PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6w6f RCSB], [http://www.ebi.ac.uk/pdbsum/6w6f PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6w6f ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Shen H]]
		+	[[Category: Stoute J]]

OCA at 03:57, 13 May 2020

OCA — Wed, 13 May 2020 03:57:28 GMT

←Older revision		Revision as of 03:57, 13 May 2020
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6w6f is ON HOLD	+	The entry 6w6f is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6w6f" [edit=sysop:move=sysop]

OCA — Fri, 27 Mar 2020 08:25:36 GMT

Protected "6w6f" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:25, 27 March 2020

OCA: New page: '''Unreleased structure''' The entry 6w6f is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Fri, 27 Mar 2020 08:25:34 GMT

New page: '''Unreleased structure''' The entry 6w6f is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6w6f is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]