6o16 - Revision history

OCA at 14:50, 13 March 2024

OCA — Wed, 13 Mar 2024 14:50:10 GMT

←Older revision		Revision as of 14:50, 13 March 2024
Line 3:		Line 3:
	<StructureSection load='6o16' size='340' side='right'caption='[[6o16]], [[Resolution\|resolution]] 2.88Å' scene=''>		<StructureSection load='6o16' size='340' side='right'caption='[[6o16]], [[Resolution\|resolution]] 2.88Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6o16]] is a 4 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=6O16 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6O16 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6o16]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6O16 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6O16 FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~Dhx37 (~~[~~http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=10090 LK3 transgenic mice])~~</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]] 2.875Å</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=6o16 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6o16 OCA], [~~http~~://pdbe.org/6o16 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6o16 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6o16 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6o16 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=6o16 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6o16 OCA], [https://pdbe.org/6o16 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6o16 RCSB], [https://www.ebi.ac.uk/pdbsum/6o16 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6o16 ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/Q6NZL1_MOUSE Q6NZL1_MOUSE]
-	Eukaryotic ribosome biogenesis is a highly orchestrated process involving numerous assembly factors including ATP-dependent RNA helicases. The DEAH helicase DHX37 (Dhr1 in yeast) is activated by the ribosome biogenesis factor UTP14 to facilitate maturation of the small ribosomal subunit. We report the crystal structure of DHX37 in complex with single-stranded RNA, revealing a canonical DEAH ATPase/helicase architecture complemented by a structurally unique C-terminal domain. Structural comparisons of the nucleotide-free DHX37-RNA complex with DEAH helicases bound to RNA and ATP analogs reveal conformational changes resulting in a register shift in the bound RNA, suggesting a mechanism for ATP-dependent, 3'-5' RNA translocation. We further show that a conserved sequence motif in UTP14 interacts with and activates DHX37 by stimulating its ATPase activity and enhancing RNA binding. In turn, the C-terminal domain of DHX37 is required, but not sufficient, for interaction with UTP14 in vitro and is essential for ribosome biogenesis in vivo. Together, these results shed light on the mechanism of DHX37 and the function of UTP14 in controlling its recruitment and activity during ribosome biogenesis.	+
-		+
-	Molecular mechanism of the RNA helicase DHX37 and its activation by UTP14 in ribosome biogenesis.,Boneberg F, Brandmann T, Kobel L, van den Heuvel J, Bargsten K, Bammert L, Kutay U, Jinek M RNA. 2019 Mar 25. pii: ~~rna.069609.118. doi: 10.1261~~/~~rna.069609.118. PMID:30910870<ref>PMID:30910870<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 6o16" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Lk3 transgenic mice~~]]	+	[[Category: Mus musculus]]
-	[[Category: Bammert, L]]	+	[[Category: Synthetic construct]]
-	[[Category: Bargsten, K]]	+	[[Category: Bammert L]]
-	[[Category: Boneberg, F]]	+	[[Category: Bargsten K]]
-	[[Category: Brandmann, T]]	+	[[Category: Boneberg F]]
-	~~[[Category: Heuvel, J van den~~]]	+	[[Category: Brandmann T]]
-	[[Category: Jinek, M]]	+	[[Category: Jinek M]]
-	[[Category: Kobel, L]]	+	[[Category: Kobel L]]
-	[[Category: Kutay, U]]	+	[[Category: Kutay U]]
-	[[Category: ~~Hydrolase-rna complex]]~~	+	[[Category: Van den Heuvel J]]
-	~~[[Category: Ribosome biogenesis]]~~	+
-	~~[[Category: Rna helicase]]~~	+
-	~~[[Category: Rna-dependent atpase~~]]	+

OCA at 06:40, 29 May 2019

OCA — Wed, 29 May 2019 06:40:42 GMT

←Older revision		Revision as of 06:40, 29 May 2019
Line 3:		Line 3:
	<StructureSection load='6o16' size='340' side='right'caption='[[6o16]], [[Resolution\|resolution]] 2.88Å' scene=''>		<StructureSection load='6o16' size='340' side='right'caption='[[6o16]], [[Resolution\|resolution]] 2.88Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6o16]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6O16 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6O16 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6o16]] is a 4 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=6O16 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6O16 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=6o16 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6o16 OCA], [http://pdbe.org/6o16 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6o16 RCSB], [http://www.ebi.ac.uk/pdbsum/6o16 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6o16 ProSAT]</span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">Dhx37 ([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=6o16 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6o16 OCA], [http://pdbe.org/6o16 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6o16 RCSB], [http://www.ebi.ac.uk/pdbsum/6o16 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6o16 ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 20:		Line 21:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Lk3 transgenic mice]]
	[[Category: Bammert, L]]		[[Category: Bammert, L]]
	[[Category: Bargsten, K]]		[[Category: Bargsten, K]]

OCA at 06:05, 17 April 2019

OCA — Wed, 17 Apr 2019 06:05:18 GMT

←Older revision		Revision as of 06:05, 17 April 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6o16 is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of murine DHX37 in complex with RNA==
		+	<StructureSection load='6o16' size='340' side='right'caption='[[6o16]], [[Resolution\|resolution]] 2.88Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6o16]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6O16 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6O16 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=6o16 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6o16 OCA], [http://pdbe.org/6o16 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6o16 RCSB], [http://www.ebi.ac.uk/pdbsum/6o16 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6o16 ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Eukaryotic ribosome biogenesis is a highly orchestrated process involving numerous assembly factors including ATP-dependent RNA helicases. The DEAH helicase DHX37 (Dhr1 in yeast) is activated by the ribosome biogenesis factor UTP14 to facilitate maturation of the small ribosomal subunit. We report the crystal structure of DHX37 in complex with single-stranded RNA, revealing a canonical DEAH ATPase/helicase architecture complemented by a structurally unique C-terminal domain. Structural comparisons of the nucleotide-free DHX37-RNA complex with DEAH helicases bound to RNA and ATP analogs reveal conformational changes resulting in a register shift in the bound RNA, suggesting a mechanism for ATP-dependent, 3'-5' RNA translocation. We further show that a conserved sequence motif in UTP14 interacts with and activates DHX37 by stimulating its ATPase activity and enhancing RNA binding. In turn, the C-terminal domain of DHX37 is required, but not sufficient, for interaction with UTP14 in vitro and is essential for ribosome biogenesis in vivo. Together, these results shed light on the mechanism of DHX37 and the function of UTP14 in controlling its recruitment and activity during ribosome biogenesis.

-	~~Authors:~~ Boneberg, F., Brandmann, T., Kobel, L., van den Heuvel, J., Bargsten, K., Bammert, L., Kutay, U., Jinek, M.	+	Molecular mechanism of the RNA helicase DHX37 and its activation by UTP14 in ribosome biogenesis.,Boneberg F, Brandmann T, Kobel L, van den Heuvel J, Bargsten K, Bammert L, Kutay U, Jinek M RNA. 2019 Mar 25. pii: rna.069609.118. doi: 10.1261/rna.069609.118. PMID:30910870<ref>PMID:30910870</ref>

-	~~Description: Crystal structure~~ of ~~murine DHX37 in complex with RNA~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Jinek, M]]~~	+	<div class="pdbe-citations 6o16" style="background-color:#fffaf0;"></div>
-	~~[[Category: Kutay, U]]~~	+	== References ==
-	~~[[Category: Kobel, L]]~~	+	<references/>
-	~~[[Category: Bargsten, K]]~~	+	__TOC__
-	[[Category: ~~Van Den Heuvel, J~~]]	+	</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Bammert, L]]		[[Category: Bammert, L]]
		+	[[Category: Bargsten, K]]
	[[Category: Boneberg, F]]		[[Category: Boneberg, F]]
	[[Category: Brandmann, T]]		[[Category: Brandmann, T]]
		+	[[Category: Heuvel, J van den]]
		+	[[Category: Jinek, M]]
		+	[[Category: Kobel, L]]
		+	[[Category: Kutay, U]]
		+	[[Category: Hydrolase-rna complex]]
		+	[[Category: Ribosome biogenesis]]
		+	[[Category: Rna helicase]]
		+	[[Category: Rna-dependent atpase]]

OCA at 04:57, 27 March 2019

OCA — Wed, 27 Mar 2019 04:57:31 GMT

←Older revision		Revision as of 04:57, 27 March 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6o16 is ON HOLD	+	The entry 6o16 is ON HOLD until Paper Publication

	Authors: Boneberg, F., Brandmann, T., Kobel, L., van den Heuvel, J., Bargsten, K., Bammert, L., Kutay, U., Jinek, M.		Authors: Boneberg, F., Brandmann, T., Kobel, L., van den Heuvel, J., Bargsten, K., Bammert, L., Kutay, U., Jinek, M.
Line 9:		Line 9:
	[[Category: Jinek, M]]		[[Category: Jinek, M]]
	[[Category: Kutay, U]]		[[Category: Kutay, U]]
-	[[Category: Bammert, L]]
	[[Category: Kobel, L]]		[[Category: Kobel, L]]
-	[[Category: Boneberg, F]]
-	[[Category: Brandmann, T]]
	[[Category: Bargsten, K]]		[[Category: Bargsten, K]]
	[[Category: Van Den Heuvel, J]]		[[Category: Van Den Heuvel, J]]
		+	[[Category: Bammert, L]]
		+	[[Category: Boneberg, F]]
		+	[[Category: Brandmann, T]]

OCA at 05:38, 6 March 2019

OCA — Wed, 06 Mar 2019 05:38:46 GMT

←Older revision		Revision as of 05:38, 6 March 2019
Line 3:		Line 3:
	The entry 6o16 is ON HOLD		The entry 6o16 is ON HOLD

-	Authors: Boneberg, F., Brandmann, T., Kobel, L., Bargsten, K., Jinek, M.	+	Authors: Boneberg, F., Brandmann, T., Kobel, L., van den Heuvel, J., Bargsten, K., Bammert, L., Kutay, U., Jinek, M.

	Description: Crystal structure of murine DHX37 in complex with RNA		Description: Crystal structure of murine DHX37 in complex with RNA
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Jinek, M]]		[[Category: Jinek, M]]
		+	[[Category: Kutay, U]]
		+	[[Category: Bammert, L]]
	[[Category: Kobel, L]]		[[Category: Kobel, L]]
-	[[Category: Bargsten, K]]
	[[Category: Boneberg, F]]		[[Category: Boneberg, F]]
	[[Category: Brandmann, T]]		[[Category: Brandmann, T]]
		+	[[Category: Bargsten, K]]
		+	[[Category: Van Den Heuvel, J]]

OCA: Protected "6o16" [edit=sysop:move=sysop]

OCA — Wed, 27 Feb 2019 13:49:13 GMT

Protected "6o16" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:49, 27 February 2019

OCA: New page: '''Unreleased structure''' The entry 6o16 is ON HOLD Authors: Boneberg, F., Brandmann, T., Kobel, L., Bargsten, K., Jinek, M. Description: Crystal structure of murine DHX37 in complex ...

OCA — Wed, 27 Feb 2019 13:49:11 GMT

New page: '''Unreleased structure''' The entry 6o16 is ON HOLD Authors: Boneberg, F., Brandmann, T., Kobel, L., Bargsten, K., Jinek, M. Description: Crystal structure of murine DHX37 in complex ...

New page

'''Unreleased structure'''

The entry 6o16 is ON HOLD

Authors: Boneberg, F., Brandmann, T., Kobel, L., Bargsten, K., Jinek, M.

Description: Crystal structure of murine DHX37 in complex with RNA
[[Category: Unreleased Structures]]
[[Category: Jinek, M]]
[[Category: Kobel, L]]
[[Category: Bargsten, K]]
[[Category: Boneberg, F]]
[[Category: Brandmann, T]]