6ibq - Revision history

OCA at 11:51, 24 January 2024

2024-01-24T11:51:11Z

←Older revision		Revision as of 11:51, 24 January 2024
Line 3:		Line 3:
	<StructureSection load='6ibq' size='340' side='right'caption='[[6ibq]], [[Resolution\|resolution]] 1.55Å' scene=''>		<StructureSection load='6ibq' size='340' side='right'caption='[[6ibq]], [[Resolution\|resolution]] 1.55Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ibq]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IBQ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6IBQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ibq]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Rattus Rattus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IBQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6IBQ FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.55Å</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=6ibq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ibq OCA], [~~http~~://pdbe.org/6ibq PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6ibq RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6ibq PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6ibq ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=6ibq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ibq OCA], [https://pdbe.org/6ibq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ibq RCSB], [https://www.ebi.ac.uk/pdbsum/6ibq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ibq ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 21:		Line 22:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Lorber, B]]	+	[[Category: Rattus]]
-	[[Category: Olieric, V]]	+	[[Category: Lorber B]]
-	[[Category: Sauter, C]]	+	[[Category: Olieric V]]
-	[[Category: Wijn, R ~~de]]~~	+	[[Category: Sauter C]]
-	~~[[Category: Chipx]]~~	+	[[Category: De Wijn R]]
-	~~[[Category: Gou pair]]~~	+
-	~~[[Category: Rna]]~~	+
-	~~[[Category: Rna duplex~~]]	+

OCA at 06:35, 29 May 2019

2019-05-29T06:35:30Z

←Older revision		Revision as of 06:35, 29 May 2019
Line 9:		Line 9:
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
-	~~The crystal structure~~ of ~~the RNA duplex [r(CGUGAUCG)dC]2 has been solved at~~ a ~~resolution~~ of ~~0.97 A. The model has been refined to R~~-~~work~~ and R-~~free of 14~~.~~88% and 19.54% for 23,838 independent reflections. The base~~-~~pairing scheme forces the 5~~'~~-rC to be excluded from the helix~~ and ~~to be disordered. In the crystals~~, ~~the sequence promotes the formation of two GoU wobble pairs that cluster around~~ a ~~crystallographic threefold axis in two different ways. In the first contact type~~, ~~the GoU pairs are exclusively surrounded by water molecules, whereas in the other contact type, the three amino groups of the guanine residues of the symmetry~~-~~related GoU pairs trap~~ a ~~sulfate ion. This work provides the first example~~ of ~~the interaction of a GoU pair~~ with ~~a sulfate ion in a helical context~~. ~~Despite the negative charge on the polynucleotide backbone~~, the ~~guanine amino N2 is able to attract negatively charged groups that could, in the folding~~ of ~~complex RNA molecules, belong to a negative phosphodiester group from a neighboring strand~~ and~~, in a~~ RNA~~-protein complex~~, ~~to a negative carboxyl group~~ of ~~an aspartate or glutamate side chain~~.	+	Determining optimal conditions for the production of well diffracting crystals is a key step in every biocrystallography project. Here, a microfluidic device is described that enables the production of crystals by counter-diffusion and their direct on-chip analysis by serial crystallography at room temperature. Nine 'non-model' and diverse biomacromolecules, including seven soluble proteins, a membrane protein and an RNA duplex, were crystallized and treated on-chip with a variety of standard techniques including micro-seeding, crystal soaking with ligands and crystal detection by fluorescence. Furthermore, the crystal structures of four proteins and an RNA were determined based on serial data collected on four synchrotron beamlines, demonstrating the general applicability of this multipurpose chip concept.

-	A ~~sulfate pocket formed~~ by ~~three GoU pairs in the 0~~.97 A ~~resolution X~~-~~ray structure of a nonameric RNA.~~,~~Masquida~~ B, Sauter C~~, Westhof E RNA~~. ~~1999 Oct~~;5(10):~~1384~~-95. PMID:~~10573129~~<ref>PMID:~~10573129~~</ref>	+	A simple and versatile microfluidic device for efficient biomacromolecule crystallization and structural analysis by serial crystallography.,de Wijn R, Hennig O, Roche J, Engilberge S, Rollet K, Fernandez-Millan P, Brillet K, Betat H, Morl M, Roussel A, Girard E, Mueller-Dieckmann C, Fox GC, Olieric V, Gavira JA, Lorber B, Sauter C IUCrJ. 2019 Apr 19;6(Pt 3):454-464. doi: 10.1107/S2052252519003622. eCollection, 2019 May 1. PMID:31098026<ref>PMID:31098026</ref>

	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>

OCA at 08:49, 1 May 2019

2019-05-01T08:49:12Z

←Older revision		Revision as of 08:49, 1 May 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6ibq is ~~ON HOLD~~	+	==Structure of a nonameric RNA duplex at room temperature in ChipX microfluidic device==
		+	<StructureSection load='6ibq' size='340' side='right'caption='[[6ibq]], [[Resolution\|resolution]] 1.55Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6ibq]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IBQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6IBQ FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=6ibq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ibq OCA], [http://pdbe.org/6ibq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ibq RCSB], [http://www.ebi.ac.uk/pdbsum/6ibq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ibq ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The crystal structure of the RNA duplex [r(CGUGAUCG)dC]2 has been solved at a resolution of 0.97 A. The model has been refined to R-work and R-free of 14.88% and 19.54% for 23,838 independent reflections. The base-pairing scheme forces the 5'-rC to be excluded from the helix and to be disordered. In the crystals, the sequence promotes the formation of two GoU wobble pairs that cluster around a crystallographic threefold axis in two different ways. In the first contact type, the GoU pairs are exclusively surrounded by water molecules, whereas in the other contact type, the three amino groups of the guanine residues of the symmetry-related GoU pairs trap a sulfate ion. This work provides the first example of the interaction of a GoU pair with a sulfate ion in a helical context. Despite the negative charge on the polynucleotide backbone, the guanine amino N2 is able to attract negatively charged groups that could, in the folding of complex RNA molecules, belong to a negative phosphodiester group from a neighboring strand and, in a RNA-protein complex, to a negative carboxyl group of an aspartate or glutamate side chain.

-	~~Authors: de Wijn, R~~.~~, Olieric, V~~., ~~Lorber,~~ B., Sauter, C.	+	A sulfate pocket formed by three GoU pairs in the 0.97 A resolution X-ray structure of a nonameric RNA.,Masquida B, Sauter C, Westhof E RNA. 1999 Oct;5(10):1384-95. PMID:10573129<ref>PMID:10573129</ref>

-	~~Description: Structure of~~ a ~~nonameric RNA duplex at room temperature in ChipX microfluidic device~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6ibq" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Lorber, B]]
	[[Category: Olieric, V]]		[[Category: Olieric, V]]
	[[Category: Sauter, C]]		[[Category: Sauter, C]]
-	[[Category: ~~Lorber~~, B]]	+	[[Category: Wijn, R de]]
-	[[Category: ~~De Wijn, R~~]]	+	[[Category: Chipx]]
		+	[[Category: Gou pair]]
		+	[[Category: Rna]]
		+	[[Category: Rna duplex]]

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

2018-12-12T05:06:08Z

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

←Older revision

Revision as of 05:06, 12 December 2018

OCA: New page: '''Unreleased structure''' The entry 6ibq is ON HOLD Authors: de Wijn, R., Olieric, V., Lorber, B., Sauter, C. Description: Structure of a nonameric RNA duplex at room temperature in C...

2018-12-12T05:06:07Z

New page: '''Unreleased structure''' The entry 6ibq is ON HOLD Authors: de Wijn, R., Olieric, V., Lorber, B., Sauter, C. Description: Structure of a nonameric RNA duplex at room temperature in C...

New page

'''Unreleased structure'''

The entry 6ibq is ON HOLD

Authors: de Wijn, R., Olieric, V., Lorber, B., Sauter, C.

Description: Structure of a nonameric RNA duplex at room temperature in ChipX microfluidic device
[[Category: Unreleased Structures]]
[[Category: Olieric, V]]
[[Category: Sauter, C]]
[[Category: Lorber, B]]
[[Category: De Wijn, R]]