5v1k - Revision history

OCA at 10:05, 22 May 2024

OCA — Wed, 22 May 2024 10:05:48 GMT

←Older revision		Revision as of 10:05, 22 May 2024
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	<StructureSection load='5v1k' size='340' side='right'caption='[[5v1k]], [[Resolution\|resolution]] 1.18Å' scene=''>		<StructureSection load='5v1k' size='340' side='right'caption='[[5v1k]], [[Resolution\|resolution]] 1.18Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5v1k]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V1K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5V1K FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5v1k]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V1K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5V1K FirstGlance]. <br>
-	</td></tr><tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non~~-~~Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=5BU:5-BROMO-URIDINE-5-MONOPHOSPHATE'>5BU</scene>, <scene name='pdbligand=8RJ:'>8RJ</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]] 1.18Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5BU:5-BROMO-URIDINE-5-MONOPHOSPHATE'>5BU</scene>, <scene name='pdbligand=8RJ:(R)-1-(2,3-DIHYDROXYPROPYL)-THYMINE'>8RJ</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=5v1k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v1k OCA], [https://pdbe.org/5v1k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5v1k RCSB], [https://www.ebi.ac.uk/pdbsum/5v1k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5v1k 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=5v1k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v1k OCA], [https://pdbe.org/5v1k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5v1k RCSB], [https://www.ebi.ac.uk/pdbsum/5v1k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5v1k ProSAT]</span></td></tr>
	</table>		</table>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Egli, M~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Pallan, P S~~]]	+	[[Category: Egli M]]
-	[[Category: ~~Glycol nucleic acid]]~~	+	[[Category: Pallan PS]]
-	~~[[Category: Gna]]~~	+
-	~~[[Category: Modified rna]]~~	+
-	~~[[Category: Nuclease stability]]~~	+
-	~~[[Category: Rgna]]~~	+
-	~~[[Category: Rna]]~~	+
-	~~[[Category: Rna x-ray structure~~]]	+

OCA at 09:49, 22 June 2022

OCA — Wed, 22 Jun 2022 09:49:48 GMT

←Older revision		Revision as of 09:49, 22 June 2022
Line 3:		Line 3:
	<StructureSection load='5v1k' size='340' side='right'caption='[[5v1k]], [[Resolution\|resolution]] 1.18Å' scene=''>		<StructureSection load='5v1k' size='340' side='right'caption='[[5v1k]], [[Resolution\|resolution]] 1.18Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5v1k]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V1K OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5V1K FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5v1k]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V1K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5V1K FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5BU:5-BROMO-URIDINE-5-MONOPHOSPHATE'>5BU</scene>, <scene name='pdbligand=8RJ:'>8RJ</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5BU:5-BROMO-URIDINE-5-MONOPHOSPHATE'>5BU</scene>, <scene name='pdbligand=8RJ:'>8RJ</scene></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=5v1k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v1k OCA], [~~http~~://pdbe.org/5v1k PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5v1k RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5v1k PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5v1k 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=5v1k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v1k OCA], [https://pdbe.org/5v1k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5v1k RCSB], [https://www.ebi.ac.uk/pdbsum/5v1k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5v1k ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 08:29, 30 September 2020

OCA — Wed, 30 Sep 2020 08:29:15 GMT

←Older revision		Revision as of 08:29, 30 September 2020
Line 1:		Line 1:

	==Structure of R-GNA dodecamer==		==Structure of R-GNA dodecamer==
-	<StructureSection load='5v1k' size='340' side='right' caption='[[5v1k]], [[Resolution\|resolution]] 1.18Å' scene=''>	+	<StructureSection load='5v1k' size='340' side='right'caption='[[5v1k]], [[Resolution\|resolution]] 1.18Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5v1k]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V1K OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5V1K FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5v1k]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V1K OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5V1K FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5BU:5-BROMO-URIDINE-5-MONOPHOSPHATE'>5BU</scene>, <scene name='pdbligand=8RJ:'>8RJ</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5BU:5-BROMO-URIDINE-5-MONOPHOSPHATE'>5BU</scene>, <scene name='pdbligand=8RJ:'>8RJ</scene></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=5v1k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v1k OCA], [http://pdbe.org/5v1k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5v1k RCSB], [http://www.ebi.ac.uk/pdbsum/5v1k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5v1k ProSAT]</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=5v1k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v1k OCA], [http://pdbe.org/5v1k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5v1k RCSB], [http://www.ebi.ac.uk/pdbsum/5v1k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5v1k ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Egli, M]]		[[Category: Egli, M]]
	[[Category: Pallan, P S]]		[[Category: Pallan, P S]]

OCA at 06:02, 17 August 2017

OCA — Thu, 17 Aug 2017 06:02:45 GMT

←Older revision		Revision as of 06:02, 17 August 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5v1k is ~~ON HOLD~~	+	==Structure of R-GNA dodecamer==
		+	<StructureSection load='5v1k' size='340' side='right' caption='[[5v1k]], [[Resolution\|resolution]] 1.18Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5v1k]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V1K OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5V1K FirstGlance]. <br>
		+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=5BU:5-BROMO-URIDINE-5-MONOPHOSPHATE'>5BU</scene>, <scene name='pdbligand=8RJ:'>8RJ</scene></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=5v1k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v1k OCA], [http://pdbe.org/5v1k PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5v1k RCSB], [http://www.ebi.ac.uk/pdbsum/5v1k PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5v1k ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Here we report the investigation of glycol nucleic acid (GNA), an acyclic nucleic acid analogue, as a modification of siRNA duplexes. We evaluated the impact of (S)- or (R)-GNA nucleotide incorporation on RNA duplex structure by determining three individual crystal structures. These structures indicate that the (S)-nucleotide backbone adopts a conformation that has little impact on the overall duplex structure, while the (R)-nucleotide disrupts the phosphate backbone and hydrogen bonding of an adjacent base pair. In addition, the GNA-T nucleobase adopts a rotated conformation in which the 5-methyl group points into the minor groove, rather than the major groove as in a normal Watson-Crick base pair. This observation of reverse Watson-Crick base pairing is further supported by thermal melting analysis of GNA-C and GNA-G containing duplexes where it was demonstrated that a higher thermal stability was associated with isoguanine and isocytosine base pairing, respectively, over the canonical nucleobases. Furthermore, it was also shown that GNA nucleotide or dinucleotide incorporation increases resistance against snake venom phosphodiesterase. Consistent with the structural data, modification of an siRNA with (S)-GNA resulted in greater in vitro potencies over identical sequences containing (R)-GNA. A walk of (S)-GNA along the guide and passenger strands of a GalNAc conjugate duplex targeting mouse transthyretin (TTR) indicated that GNA is well tolerated in the seed region of both strands in vitro, resulting in an approximate 2-fold improvement in potency. Finally, these conjugate duplexes modified with GNA were capable of maintaining in vivo potency when subcutaneously injected into mice.

-	~~Authors:~~ Pallan, ~~P.S.~~, Egli, M.	+	Chirality Dependent Potency Enhancement and Structural Impact of Glycol Nucleic Acid Modification on siRNA.,Schlegel MK, Foster DJ, Kel'in AV, Zlatev I, Bisbe A, Jayaraman M, Lackey JG, Rajeev KG, Charisse K, Harp J, Pallan PS, Maier MA, Egli M, Manoharan M J Am Chem Soc. 2017 Jun 28;139(25):8537-8546. doi: 10.1021/jacs.7b02694. Epub, 2017 Jun 19. PMID:28570818<ref>PMID:28570818</ref>

-	~~Description: Structure~~ of ~~R-GNA dodecamer~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Pallan, P.S]]~~	+	<div class="pdbe-citations 5v1k" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Egli, M]]		[[Category: Egli, M]]
		+	[[Category: Pallan, P S]]
		+	[[Category: Glycol nucleic acid]]
		+	[[Category: Gna]]
		+	[[Category: Modified rna]]
		+	[[Category: Nuclease stability]]
		+	[[Category: Rgna]]
		+	[[Category: Rna]]
		+	[[Category: Rna x-ray structure]]

OCA at 19:36, 15 March 2017

OCA — Wed, 15 Mar 2017 19:36:50 GMT

←Older revision		Revision as of 19:36, 15 March 2017
Line 3:		Line 3:
	The entry 5v1k is ON HOLD		The entry 5v1k is ON HOLD

-	Authors: Pallan, P.S., Egli, M	+	Authors: Pallan, P.S., Egli, M.

	Description: Structure of R-GNA dodecamer		Description: Structure of R-GNA dodecamer

OCA: Protected "5v1k" [edit=sysop:move=sysop]

OCA — Thu, 09 Mar 2017 15:13:59 GMT

Protected "5v1k" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:13, 9 March 2017

OCA: New page: '''Unreleased structure''' The entry 5v1k is ON HOLD Authors: Pallan, P.S., Egli, M Description: Structure of R-GNA dodecamer Category: Unreleased Structures [[Category: Pallan, P....

OCA — Thu, 09 Mar 2017 15:13:58 GMT

New page: '''Unreleased structure''' The entry 5v1k is ON HOLD Authors: Pallan, P.S., Egli, M Description: Structure of R-GNA dodecamer Category: Unreleased Structures [[Category: Pallan, P....

New page

'''Unreleased structure'''

The entry 5v1k is ON HOLD

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

Description: Structure of R-GNA dodecamer
[[Category: Unreleased Structures]]
[[Category: Pallan, P.S]]
[[Category: Egli, M]]