4kze - Revision history

OCA at 09:22, 7 December 2022

2022-12-07T09:22:41Z

←Older revision		Revision as of 09:22, 7 December 2022
Line 3:		Line 3:
	<StructureSection load='4kze' size='340' side='right'caption='[[4kze]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='4kze' size='340' side='right'caption='[[4kze]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4kze]] is a 3 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=4KZE OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4KZE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4kze]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KZE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4KZE FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:~~POTASSIUM+ION~~'>K</scene>, <scene name='pdbligand=MG:~~MAGNESIUM~~+ION'>MG</scene>~~</td></tr>~~	+	</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=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=~~GTP~~:~~GUANOSINE-5-TRIPHOSPHATE~~'>~~GTP~~</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=4kze FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kze OCA], [https://pdbe.org/4kze PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4kze RCSB], [https://www.ebi.ac.uk/pdbsum/4kze PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4kze ProSAT]</span></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ivk\|3ivk]], [[4kzd\|4kzd]]~~</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=4kze FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kze OCA], [~~http~~://pdbe.org/4kze PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4kze RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4kze PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4kze ProSAT]</span></td></tr>	+
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 21:		Line 19:
	==See Also==		==See Also==
	*[[Antibody 3D structures\|Antibody 3D structures]]		*[[Antibody 3D structures\|Antibody 3D structures]]
		+	*[[3D structures of non-human antibody\|3D structures of non-human antibody]]
	== References ==		== References ==
	<references/>		<references/>
Line 26:		Line 25:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Lk3 transgenic mice~~]]	+	[[Category: Mus musculus]]
-	[[Category: Huang, H]]	+	[[Category: Huang H]]
-	[[Category: Koldobskaya, Y]]	+	[[Category: Koldobskaya Y]]
-	[[Category: Li, N]]	+	[[Category: Li N]]
-	[[Category: Piccirilli~~, J A~~]]	+	[[Category: Piccirilli JA]]
-	[[Category: Rice~~, P A~~]]	+	[[Category: Rice PA]]
-	[[Category: Suslov~~, N B]]~~	+	[[Category: Suslov NB]]
-	~~[[Category: Fluorescence]]~~	+
-	~~[[Category: Fluorophore binding]]~~	+
-	~~[[Category: G-quadruplex]]~~	+
-	~~[[Category: Immune system-rna complex~~]]	+

OCA at 08:58, 3 April 2019

2019-04-03T08:58:03Z

←Older revision		Revision as of 08:58, 3 April 2019
Line 1:		Line 1:

	==Crystal structure of an RNA aptamer in complex with Fab==		==Crystal structure of an RNA aptamer in complex with Fab==
-	<StructureSection load='4kze' size='340' side='right' caption='[[4kze]], [[Resolution\|resolution]] 2.40Å' scene=''>	+	<StructureSection load='4kze' size='340' side='right'caption='[[4kze]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4kze]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KZE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4KZE FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4kze]] is a 3 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=4KZE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4KZE FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene></td></tr>
Line 18:		Line 18:
	</div>		</div>
	<div class="pdbe-citations 4kze" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 4kze" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Antibody 3D structures\|Antibody 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Lk3 transgenic mice]]
	[[Category: Huang, H]]		[[Category: Huang, H]]
	[[Category: Koldobskaya, Y]]		[[Category: Koldobskaya, Y]]

OCA at 19:50, 11 August 2016

2016-08-11T19:50:07Z

←Older revision		Revision as of 19:50, 11 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of an RNA aptamer in complex with Fab==		==Crystal structure of an RNA aptamer in complex with Fab==
	<StructureSection load='4kze' size='340' side='right' caption='[[4kze]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='4kze' size='340' side='right' caption='[[4kze]], [[Resolution\|resolution]] 2.40Å' scene=''>
Line 6:		Line 7:
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ivk\|3ivk]], [[4kzd\|4kzd]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ivk\|3ivk]], [[4kzd\|4kzd]]</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=4kze FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kze OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4kze RCSB], [http://www.ebi.ac.uk/pdbsum/4kze PDBsum]</span></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=4kze FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kze OCA], [http://pdbe.org/4kze PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4kze RCSB], [http://www.ebi.ac.uk/pdbsum/4kze PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4kze ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 16:		Line 17:
	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>
	</div>		</div>
		+	<div class="pdbe-citations 4kze" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 12:40, 5 January 2015

2015-01-05T12:40:25Z

←Older revision		Revision as of 12:40, 5 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4kze]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KZE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4KZE FirstGlance]. <br>		<table><tr><td colspan='2'>[[4kze]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KZE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4KZE FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ivk\|3ivk]], [[4kzd\|4kzd]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ivk\|3ivk]], [[4kzd\|4kzd]]</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4kze FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kze OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4kze RCSB], [http://www.ebi.ac.uk/pdbsum/4kze PDBsum]</span></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=4kze FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kze OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4kze RCSB], [http://www.ebi.ac.uk/pdbsum/4kze PDBsum]</span></td></tr>
-	<table>	+	</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Huang, H.]]	+	[[Category: Huang, H]]
-	[[Category: Koldobskaya, Y.]]	+	[[Category: Koldobskaya, Y]]
-	[[Category: Li, N.]]	+	[[Category: Li, N]]
-	[[Category: Piccirilli, J A.]]	+	[[Category: Piccirilli, J A]]
-	[[Category: Rice, P A.]]	+	[[Category: Rice, P A]]
-	[[Category: Suslov, N B.]]	+	[[Category: Suslov, N B]]
	[[Category: Fluorescence]]		[[Category: Fluorescence]]
	[[Category: Fluorophore binding]]		[[Category: Fluorophore binding]]
	[[Category: G-quadruplex]]		[[Category: G-quadruplex]]
	[[Category: Immune system-rna complex]]		[[Category: Immune system-rna complex]]

OCA at 06:18, 9 July 2014

2014-07-09T06:18:10Z

←Older revision		Revision as of 06:18, 9 July 2014
Line 8:		Line 8:
	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4kze FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kze OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4kze RCSB], [http://www.ebi.ac.uk/pdbsum/4kze PDBsum]</span></td></tr>		<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4kze FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kze OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4kze RCSB], [http://www.ebi.ac.uk/pdbsum/4kze PDBsum]</span></td></tr>
	<table>		<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Spinach is an in vitro-selected RNA aptamer that binds a GFP-like ligand and activates its green fluorescence. Spinach is thus an RNA analog of GFP and has potentially widespread applications for in vivo labeling and imaging. We used antibody-assisted crystallography to determine the structures of Spinach both with and without bound fluorophore at 2.2-A and 2.4-A resolution, respectively. Spinach RNA has an elongated structure containing two helical domains separated by an internal bulge that folds into a G-quadruplex motif of unusual topology. The G-quadruplex motif and adjacent nucleotides comprise a partially preformed binding site for the fluorophore. The fluorophore binds in a planar conformation and makes extensive aromatic stacking and hydrogen bond interactions with the RNA. Our findings provide a foundation for structure-based engineering of new fluorophore-binding RNA aptamers.
		+
		+	A G-quadruplex-containing RNA activates fluorescence in a GFP-like fluorophore.,Huang H, Suslov NB, Li NS, Shelke SA, Evans ME, Koldobskaya Y, Rice PA, Piccirilli JA Nat Chem Biol. 2014 Jun 22. doi: 10.1038/nchembio.1561. PMID:24952597<ref>PMID:24952597</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 08:10, 18 June 2014

2014-06-18T08:10:43Z

←Older revision		Revision as of 08:10, 18 June 2014
Line 1:		Line 1:
-	'''~~Unreleased structure~~'''	+	==Crystal structure of an RNA aptamer in complex with Fab==
-		+	<StructureSection load='4kze' size='340' side='right' caption='[[4kze]], [[Resolution\|resolution]] 2.40Å' scene=''>
-	~~The entry~~ 4kze is ~~ON HOLD until Sep 01 2015~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[4kze]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KZE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4KZE FirstGlance]. <br>
-	~~Authors~~: ~~Huang~~, H., ~~Suslov~~, N.B., ~~Li, N~~., Koldobskaya, Y., ~~Rice, P~~.~~A.,~~ Piccirilli, J.A.	+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>
-		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=GTP:GUANOSINE-5-TRIPHOSPHATE'>GTP</scene></td></tr>
-	~~Description~~: ~~Crystal structure of an RNA aptamer in~~ complex ~~with Fab~~	+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3ivk\|3ivk]], [[4kzd\|4kzd]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4kze FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kze OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4kze RCSB], [http://www.ebi.ac.uk/pdbsum/4kze PDBsum]</span></td></tr>
		+	<table>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Huang, H.]]
		+	[[Category: Koldobskaya, Y.]]
		+	[[Category: Li, N.]]
		+	[[Category: Piccirilli, J A.]]
		+	[[Category: Rice, P A.]]
		+	[[Category: Suslov, N B.]]
		+	[[Category: Fluorescence]]
		+	[[Category: Fluorophore binding]]
		+	[[Category: G-quadruplex]]
		+	[[Category: Immune system-rna complex]]

OCA at 07:39, 28 May 2014

2014-05-28T07:39:56Z

←Older revision		Revision as of 07:39, 28 May 2014
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4kze is ON HOLD until ~~Paper Publication~~	+	The entry 4kze is ON HOLD until Sep 01 2015

	Authors: Huang, H., Suslov, N.B., Li, N., Koldobskaya, Y., Rice, P.A., Piccirilli, J.A.		Authors: Huang, H., Suslov, N.B., Li, N., Koldobskaya, Y., Rice, P.A., Piccirilli, J.A.

	Description: Crystal structure of an RNA aptamer in complex with Fab		Description: Crystal structure of an RNA aptamer in complex with Fab

OCA: Protected "4kze" [edit=sysop:move=sysop]

2013-06-19T12:16:16Z

Protected "4kze" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:16, 19 June 2013

OCA: New page: '''Unreleased structure''' The entry 4kze is ON HOLD until Paper Publication Authors: Huang, H., Suslov, N.B., Li, N., Koldobskaya, Y., Rice, P.A., Piccirilli, J.A. Description: Crysta...

2013-06-19T12:16:15Z

New page: '''Unreleased structure''' The entry 4kze is ON HOLD until Paper Publication Authors: Huang, H., Suslov, N.B., Li, N., Koldobskaya, Y., Rice, P.A., Piccirilli, J.A. Description: Crysta...

New page

'''Unreleased structure'''

The entry 4kze is ON HOLD until Paper Publication

Authors: Huang, H., Suslov, N.B., Li, N., Koldobskaya, Y., Rice, P.A., Piccirilli, J.A.

Description: Crystal structure of an RNA aptamer in complex with Fab