8gxc - Revision history

OCA at 17:00, 8 November 2023

OCA — Wed, 08 Nov 2023 17:00:30 GMT

←Older revision		Revision as of 17:00, 8 November 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[8gxc]] is a 7 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Streptococcus_sp. Streptococcus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8GXC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8GXC FirstGlance]. <br>		<table><tr><td colspan='2'>[[8gxc]] is a 7 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Streptococcus_sp. Streptococcus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8GXC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8GXC FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NMN:BETA-NICOTINAMIDE+RIBOSE+MONOPHOSPHATE'>NMN</scene></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]] 2.5Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NMN:BETA-NICOTINAMIDE+RIBOSE+MONOPHOSPHATE'>NMN</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=8gxc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8gxc OCA], [https://pdbe.org/8gxc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8gxc RCSB], [https://www.ebi.ac.uk/pdbsum/8gxc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8gxc 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=8gxc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8gxc OCA], [https://pdbe.org/8gxc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8gxc RCSB], [https://www.ebi.ac.uk/pdbsum/8gxc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8gxc ProSAT]</span></td></tr>
	</table>		</table>
Line 18:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 8gxc" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 8gxc" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Riboswitch 3D structures\|Riboswitch 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:34, 18 January 2023

OCA — Wed, 18 Jan 2023 07:34:28 GMT

←Older revision		Revision as of 07:34, 18 January 2023
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 8gxc is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of NAD+ -II riboswitch in complex with NMN==
		+	<StructureSection load='8gxc' size='340' side='right'caption='[[8gxc]], [[Resolution\|resolution]] 2.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[8gxc]] is a 7 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Streptococcus_sp. Streptococcus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8GXC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8GXC FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NMN:BETA-NICOTINAMIDE+RIBOSE+MONOPHOSPHATE'>NMN</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=8gxc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8gxc OCA], [https://pdbe.org/8gxc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8gxc RCSB], [https://www.ebi.ac.uk/pdbsum/8gxc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8gxc ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/SNRPA_HUMAN SNRPA_HUMAN] Binds stem loop II of U1 snRNA. It is the first snRNP to interact with pre-mRNA. This interaction is required for the subsequent binding of U2 snRNP and the U4/U6/U5 tri-snRNP. In a snRNP-free form (SF-A) may be involved in coupled pre-mRNA splicing and polyadenylation process. Binds preferentially to the 5'-UGCAC-3' motif in vitro.<ref>PMID:9848648</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Riboswitches are conserved non-coding domains in bacterial mRNA with gene regulation function that are essential for maintaining enzyme co-factor metabolism. Recently, the pnuC RNA motif was reported to selectively bind nicotinamide adenine dinucleotide (NAD+), defining a novel class of NAD+ riboswitches (NAD+-II) according to phylogenetic analysis. To reveal the three-dimensional architecture and the ligand-binding mode of this riboswitch, we solved the crystal structure of NAD+-II riboswitch in complex with NAD+. Strikingly and in contrast to class-I riboswitches that form a tight recognition pocket for the adenosine diphosphate (ADP) moiety of NAD+, the class-II riboswitches form a binding pocket for the nicotinamide mononucleotide (NMN) portion of NAD+ and display only unspecific interactions with the adenosine. We support this finding by an additional structure of the class-II RNA in complex with NMN alone. The structures define a novel RNA tertiary fold that was further confirmed by mutational analysis in combination with isothermal titration calorimetry (ITC), and 2-aminopurine-based fluorescence spectroscopic folding studies. Furthermore, we truncated the pnuC RNA motif to a short RNA helical scaffold with binding affinity comparable to the wild-type motif to allude to the potential of engineering the NAD+-II motif for biotechnological applications.

-	~~Authors: Xu~~, X.C., ~~Ren~~, A.M.	+	Structure-based investigations of the NAD+-II riboswitch.,Xu X, Egger M, Li C, Chen H, Micura R, Ren A Nucleic Acids Res. 2023 Jan 11;51(1):54-67. doi: 10.1093/nar/gkac1227. PMID:36610789<ref>PMID:36610789</ref>

-	~~Description~~: ~~novel coenzyme riboswitch in complex with its ligand~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: ~~Xu, X.C~~]]	+	<div class="pdbe-citations 8gxc" style="background-color:#fffaf0;"></div>
-	[[Category: Ren~~, A.M~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Homo sapiens]]
		+	[[Category: Large Structures]]
		+	[[Category: Streptococcus sp]]
		+	[[Category: Ren AM]]
		+	[[Category: Xu XC]]

OCA at 05:29, 3 November 2022

OCA — Thu, 03 Nov 2022 05:29:56 GMT

←Older revision		Revision as of 05:29, 3 November 2022
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 8gxc is ON HOLD	+	The entry 8gxc is ON HOLD until Paper Publication

	Authors: Xu, X.C., Ren, A.M.		Authors: Xu, X.C., Ren, A.M.

-	Description: ~~new~~ coenzyme riboswitch in complex with its ligand	+	Description: novel coenzyme riboswitch in complex with its ligand
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Xu, X.C]]		[[Category: Xu, X.C]]
	[[Category: Ren, A.M]]		[[Category: Ren, A.M]]

OCA: Protected "8gxc" [edit=sysop:move=sysop]

OCA — Wed, 28 Sep 2022 04:52:21 GMT

Protected "8gxc" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:52, 28 September 2022

OCA: New page: '''Unreleased structure''' The entry 8gxc is ON HOLD Authors: Xu, X.C., Ren, A.M. Description: new coenzyme riboswitch in complex with its ligand Category: Unreleased Structures [[...

OCA — Wed, 28 Sep 2022 04:52:19 GMT

New page: '''Unreleased structure''' The entry 8gxc is ON HOLD Authors: Xu, X.C., Ren, A.M. Description: new coenzyme riboswitch in complex with its ligand Category: Unreleased Structures [[...

New page

'''Unreleased structure'''

The entry 8gxc is ON HOLD

Authors: Xu, X.C., Ren, A.M.

Description: new coenzyme riboswitch in complex with its ligand
[[Category: Unreleased Structures]]
[[Category: Xu, X.C]]
[[Category: Ren, A.M]]