7jjf - Revision history

OCA at 15:04, 18 October 2023

OCA — Wed, 18 Oct 2023 15:04:57 GMT

←Older revision		Revision as of 15:04, 18 October 2023
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	==Sarcin-ricin loop with modified residue.==		==Sarcin-ricin loop with modified residue.==
-	<StructureSection load='7jjf' size='340' side='right'caption='[[7jjf]]' scene=''>	+	<StructureSection load='7jjf' size='340' side='right'caption='[[7jjf]], [[Resolution\|resolution]] 1.20Å' 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=7JJF OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=7JJF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7jjf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7JJF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7JJF 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=7jjf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7jjf OCA], [~~http~~://pdbe.org/7jjf PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=7jjf RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/7jjf PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=7jjf ProSAT]</span></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]] 1.2Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=VC7:5-O-[(R)-hydroxy(methyl)phosphoryl]guanosine'>VC7</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=7jjf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7jjf OCA], [https://pdbe.org/7jjf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7jjf RCSB], [https://www.ebi.ac.uk/pdbsum/7jjf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7jjf ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	GNRA (N = A, C, G, or U; R = A or G) tetraloops are common RNA secondary structural motifs and feature a phosphate stacked atop a nucleobase. The rRNA sarcin/ricin loop (SRL) is capped by GApGA, and the phosphate p stacks on G. We recently found that regiospecific incorporation of a single dithiophosphate (PS2) but not a monothiophosphate (PSO) instead of phosphate in the backbone of RNA aptamers dramatically increases the binding affinity for their targets. In the RNA:thrombin complex, the key contribution to the 1000-fold tighter binding stems from an edge-on contact between PS2 and a phenylalanine ring. Here we investigated the consequences of replacing the SRL phosphate engaged in a face-on interaction with guanine with either PS2 or PSO for stability. We found that PS2...G and Rp-PSO...G contacts stabilize modified SRLs compared to the parent loop to unexpected levels: up to 6.3 degrees C in melting temperature Tm and -4.7 kcal/mol in DeltaDeltaG degrees . Crystal structures demonstrate that the vertical distance to guanine for the closest sulfur is just 0.05 A longer on average compared to that of oxygen despite the larger van der Waals radius of the former (1.80 A for S vs 1.52 A for O). The higher stability is enthalpy-based, and the negative charge as assessed by a neutral methylphosphonate modification plays only a minor role. Quantum mechanical/molecular mechanical calculations are supportive of favorable dispersion attraction interactions by sulfur making the dominant contribution. A stacking interaction between phosphate and guanine (SRL) or uracil (U-turn) is also found in newly classified RNA tetraloop families besides GNRA.
		+
		+	Incorporating a Thiophosphate Modification into a Common RNA Tetraloop Motif Causes an Unanticipated Stability Boost.,Pallan PS, Lybrand TP, Schlegel MK, Harp JM, Jahns H, Manoharan M, Egli M Biochemistry. 2020 Dec 15;59(49):4627-4637. doi: 10.1021/acs.biochem.0c00685., Epub 2020 Dec 4. PMID:33275419<ref>PMID:33275419</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7jjf" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Escherichia coli]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Egli M]]		[[Category: Egli M]]
	[[Category: Harp JM]]		[[Category: Harp JM]]
	[[Category: Pallan PS]]		[[Category: Pallan PS]]

OCA at 10:40, 24 December 2020

OCA — Thu, 24 Dec 2020 10:40:38 GMT

←Older revision		Revision as of 10:40, 24 December 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 7jjf ~~is ON HOLD until Paper Publication~~	+	==Sarcin-ricin loop with modified residue.==
-		+	<StructureSection load='7jjf' size='340' side='right'caption='[[7jjf]]' scene=''>
-	~~Authors~~: ~~Harp~~, J.M., ~~Pallan~~, P.S., ~~Egli, M~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7JJF OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=7JJF FirstGlance]. <br>
-	~~Description~~: ~~Sarcin~~-~~ricin loop with modified residue~~.	+	</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=7jjf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7jjf OCA], [http://pdbe.org/7jjf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=7jjf RCSB], [http://www.ebi.ac.uk/pdbsum/7jjf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=7jjf ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: ~~Pallan, P.S~~]]	+	__TOC__
-	[[Category: Harp~~, J.M~~]]	+	</StructureSection>
-	[[Category: ~~Egli, M~~]]	+	[[Category: Large Structures]]
		+	[[Category: Egli M]]
		+	[[Category: Harp JM]]
		+	[[Category: Pallan PS]]

OCA at 07:38, 9 September 2020

OCA — Wed, 09 Sep 2020 07:38:34 GMT

←Older revision		Revision as of 07:38, 9 September 2020
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7jjf is ON HOLD	+	The entry 7jjf is ON HOLD until Paper Publication

	Authors: Harp, J.M., Pallan, P.S., Egli, M.		Authors: Harp, J.M., Pallan, P.S., Egli, M.

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

OCA — Wed, 05 Aug 2020 04:14:25 GMT

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

←Older revision

Revision as of 04:14, 5 August 2020

OCA: New page: '''Unreleased structure''' The entry 7jjf is ON HOLD Authors: Harp, J.M., Pallan, P.S., Egli, M. Description: Sarcin-ricin loop with modified residue. [[Category: Unreleased Structures...

OCA — Wed, 05 Aug 2020 04:14:24 GMT

New page: '''Unreleased structure''' The entry 7jjf is ON HOLD Authors: Harp, J.M., Pallan, P.S., Egli, M. Description: Sarcin-ricin loop with modified residue. [[Category: Unreleased Structures...

New page

'''Unreleased structure'''

The entry 7jjf is ON HOLD

Authors: Harp, J.M., Pallan, P.S., Egli, M.

Description: Sarcin-ricin loop with modified residue.
[[Category: Unreleased Structures]]
[[Category: Pallan, P.S]]
[[Category: Harp, J.M]]
[[Category: Egli, M]]