4gma - Revision history

OCA at 11:32, 1 March 2024

2024-03-01T11:32:33Z

←Older revision		Revision as of 11:32, 1 March 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4gma]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Marine_metagenome Marine metagenome]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GMA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4GMA FirstGlance]. <br>		<table><tr><td colspan='2'>[[4gma]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Marine_metagenome Marine metagenome]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GMA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4GMA FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=B1Z:ADENOSYLCOBALAMIN'>B1Z</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]] 3.94Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=B1Z:ADENOSYLCOBALAMIN'>B1Z</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=4gma FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gma OCA], [https://pdbe.org/4gma PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4gma RCSB], [https://www.ebi.ac.uk/pdbsum/4gma PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4gma 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=4gma FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gma OCA], [https://pdbe.org/4gma PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4gma RCSB], [https://www.ebi.ac.uk/pdbsum/4gma PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4gma ProSAT]</span></td></tr>
	</table>		</table>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Structures of riboswitch receptor domains bound to their effector have shown how messenger RNAs recognize diverse small molecules, but mechanistic details linking the structures to the regulation of gene expression remain elusive. To address this, here we solve crystal structures of two different classes of cobalamin (vitamin B(12))-binding riboswitches that include the structural switch of the downstream regulatory domain. These classes share a common cobalamin-binding core, but use distinct peripheral extensions to recognize different B(12) derivatives. In each case, recognition is accomplished through shape complementarity between the RNA and cobalamin, with relatively few hydrogen bonding interactions that typically govern RNA-small molecule recognition. We show that a composite cobalamin-RNA scaffold stabilizes an unusual long-range intramolecular kissing-loop interaction that controls mRNA expression. This is the first, to our knowledge, riboswitch crystal structure detailing how the receptor and regulatory domains communicate in a ligand-dependent fashion to regulate mRNA expression.
-
-	B12 cofactors directly stabilize an mRNA regulatory switch.,Johnson JE Jr, Reyes FE, Polaski JT, Batey RT Nature. 2012 Dec 6;492(7427):133-7. doi: 10.1038/nature11607. Epub 2012 Oct 14. PMID:23064232<ref>PMID:23064232</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 4gma" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Riboswitch 3D structures\|Riboswitch 3D structures]]		*[[Riboswitch 3D structures\|Riboswitch 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 07:05, 26 October 2022

2022-10-26T07:05:46Z

←Older revision		Revision as of 07:05, 26 October 2022
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	<StructureSection load='4gma' size='340' side='right'caption='[[4gma]], [[Resolution\|resolution]] 3.94Å' scene=''>		<StructureSection load='4gma' size='340' side='right'caption='[[4gma]], [[Resolution\|resolution]] 3.94Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4gma]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GMA OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4GMA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4gma]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Marine_metagenome Marine metagenome]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GMA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4GMA FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=B1Z:ADENOSYLCOBALAMIN'>B1Z</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=B1Z:ADENOSYLCOBALAMIN'>B1Z</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=4gma FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gma OCA], [~~http~~://pdbe.org/4gma PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4gma RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4gma PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4gma 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=4gma FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gma OCA], [https://pdbe.org/4gma PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4gma RCSB], [https://www.ebi.ac.uk/pdbsum/4gma PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4gma ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 18:		Line 18:

	==See Also==		==See Also==
-	*[[Riboswitch\|Riboswitch]]	+	*[[Riboswitch 3D structures\|Riboswitch 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 24:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Batey, R T~~]]	+	[[Category: Marine metagenome]]
-	[[Category: ~~Johnson, J E~~]]	+	[[Category: Batey RT]]
-	[[Category: ~~Polaski, J T~~]]	+	[[Category: Johnson JE]]
-	[[Category: ~~Reyes, F E~~]]	+	[[Category: Polaski JT]]
-	[[Category: ~~Adenosylcobalamin]]~~	+	[[Category: Reyes FE]]
-	~~[[Category: Adocbl]]~~	+
-	~~[[Category: Riboswitch]]~~	+
-	~~[[Category: Rna~~]]	+

OCA at 18:00, 14 August 2019

2019-08-14T18:00:19Z

←Older revision		Revision as of 18:00, 14 August 2019
Line 1:		Line 1:

	==Crystal structure of the adenosylcobalamin riboswitch==		==Crystal structure of the adenosylcobalamin riboswitch==
-	<StructureSection load='4gma' size='340' side='right' caption='[[4gma]], [[Resolution\|resolution]] 3.94Å' scene=''>	+	<StructureSection load='4gma' size='340' side='right'caption='[[4gma]], [[Resolution\|resolution]] 3.94Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4gma]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GMA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4GMA FirstGlance]. <br>		<table><tr><td colspan='2'>[[4gma]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GMA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4GMA FirstGlance]. <br>
Line 23:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Batey, R T]]		[[Category: Batey, R T]]
	[[Category: Johnson, J E]]		[[Category: Johnson, J E]]

OCA at 19:47, 15 December 2016

2016-12-15T19:47:02Z

←Older revision		Revision as of 19:47, 15 December 2016
Line 1:		Line 1:
		+
	==Crystal structure of the adenosylcobalamin riboswitch==		==Crystal structure of the adenosylcobalamin riboswitch==
	<StructureSection load='4gma' size='340' side='right' caption='[[4gma]], [[Resolution\|resolution]] 3.94Å' scene=''>		<StructureSection load='4gma' size='340' side='right' caption='[[4gma]], [[Resolution\|resolution]] 3.94Å' scene=''>
Line 4:		Line 5:
	<table><tr><td colspan='2'>[[4gma]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GMA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4GMA FirstGlance]. <br>		<table><tr><td colspan='2'>[[4gma]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GMA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4GMA FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=B1Z:ADENOSYLCOBALAMIN'>B1Z</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=B1Z:ADENOSYLCOBALAMIN'>B1Z</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=4gma FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gma OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4gma RCSB], [http://www.ebi.ac.uk/pdbsum/4gma 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=4gma FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gma OCA], [http://pdbe.org/4gma PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4gma RCSB], [http://www.ebi.ac.uk/pdbsum/4gma PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4gma ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 14:		Line 15:
	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 4gma" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==

OCA at 09:01, 10 December 2014

2014-12-10T09:01:28Z

←Older revision		Revision as of 09:01, 10 December 2014
Line 1:		Line 1:
-	[[~~Image:~~4gma.~~png~~\|~~left\|200px~~]]	+	==Crystal structure of the adenosylcobalamin riboswitch==
		+	<StructureSection load='4gma' size='340' side='right' caption='[[4gma]], [[Resolution\|resolution]] 3.94Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4gma]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GMA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4GMA FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=B1Z:ADENOSYLCOBALAMIN'>B1Z</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=4gma FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4gma OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4gma RCSB], [http://www.ebi.ac.uk/pdbsum/4gma PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Structures of riboswitch receptor domains bound to their effector have shown how messenger RNAs recognize diverse small molecules, but mechanistic details linking the structures to the regulation of gene expression remain elusive. To address this, here we solve crystal structures of two different classes of cobalamin (vitamin B(12))-binding riboswitches that include the structural switch of the downstream regulatory domain. These classes share a common cobalamin-binding core, but use distinct peripheral extensions to recognize different B(12) derivatives. In each case, recognition is accomplished through shape complementarity between the RNA and cobalamin, with relatively few hydrogen bonding interactions that typically govern RNA-small molecule recognition. We show that a composite cobalamin-RNA scaffold stabilizes an unusual long-range intramolecular kissing-loop interaction that controls mRNA expression. This is the first, to our knowledge, riboswitch crystal structure detailing how the receptor and regulatory domains communicate in a ligand-dependent fashion to regulate mRNA expression.

-	~~{{STRUCTURE_4gma\| PDB=4gma \| SCENE= }}~~	+	B12 cofactors directly stabilize an mRNA regulatory switch.,Johnson JE Jr, Reyes FE, Polaski JT, Batey RT Nature. 2012 Dec 6;492(7427):133-7. doi: 10.1038/nature11607. Epub 2012 Oct 14. PMID:23064232<ref>PMID:23064232</ref>

-	~~===Crystal structure~~ of the ~~adenosylcobalamin riboswitch===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-	~~{{ABSTRACT_PUBMED_23064232}}~~	+	==See Also==
-		+	*[[Riboswitch\|Riboswitch]]
-	==~~About this Structure~~==	+	== References ==
-	[[~~4gma~~]] ~~is a 1 chain structure. Full crystallographic information is available from [http:~~//~~oca.weizmann.ac.il/oca-bin/ocashort?id=4GMA OCA].~~	+	<references/>
-	[[Category: Batey, R T.]]	+	__TOC__
-	[[Category: Johnson, J E.]]	+	</StructureSection>
-	[[Category: Polaski, J T.]]	+	[[Category: Batey, R T]]
-	[[Category: Reyes, F E.]]	+	[[Category: Johnson, J E]]
		+	[[Category: Polaski, J T]]
		+	[[Category: Reyes, F E]]
	[[Category: Adenosylcobalamin]]		[[Category: Adenosylcobalamin]]
	[[Category: Adocbl]]		[[Category: Adocbl]]
	[[Category: Riboswitch]]		[[Category: Riboswitch]]
	[[Category: Rna]]		[[Category: Rna]]

OCA at 06:52, 2 January 2013

2013-01-02T06:52:14Z

←Older revision		Revision as of 06:52, 2 January 2013
Line 1:		Line 1:
-	[[Image:4gma.~~jpg~~\|left\|200px]]	+	[[Image:4gma.png\|left\|200px]]

	{{STRUCTURE_4gma\| PDB=4gma \| SCENE= }}		{{STRUCTURE_4gma\| PDB=4gma \| SCENE= }}
Line 5:		Line 5:
	===Crystal structure of the adenosylcobalamin riboswitch===		===Crystal structure of the adenosylcobalamin riboswitch===

		+	{{ABSTRACT_PUBMED_23064232}}

	==About this Structure==		==About this Structure==

OCA at 07:14, 17 October 2012

2012-10-17T07:14:02Z

←Older revision		Revision as of 07:14, 17 October 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:4gma.jpg\|left\|200px]]

-	~~The entry~~ 4gma ~~is ON HOLD~~ ~~until Paper Publication~~	+	{{STRUCTURE_4gma\| PDB=4gma \| SCENE= }}

-	~~Authors: Reyes, F.E., Johnson, J.E., Polaski, J.T., Batey, R.T.~~	+	===Crystal structure of the adenosylcobalamin riboswitch===

-	~~Description: Crystal~~ structure ~~of the adenosylcobalamin riboswitch~~	+
		+	==About this Structure==
		+	[[4gma]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4GMA OCA].
		+	[[Category: Batey, R T.]]
		+	[[Category: Johnson, J E.]]
		+	[[Category: Polaski, J T.]]
		+	[[Category: Reyes, F E.]]
		+	[[Category: Adenosylcobalamin]]
		+	[[Category: Adocbl]]
		+	[[Category: Riboswitch]]
		+	[[Category: Rna]]

OCA at 05:44, 3 October 2012

2012-10-03T05:44:07Z

←Older revision		Revision as of 05:44, 3 October 2012
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 4gma is ON HOLD	+	The entry 4gma is ON HOLD until Paper Publication

	Authors: Reyes, F.E., Johnson, J.E., Polaski, J.T., Batey, R.T.		Authors: Reyes, F.E., Johnson, J.E., Polaski, J.T., Batey, R.T.

	Description: Crystal structure of the adenosylcobalamin riboswitch		Description: Crystal structure of the adenosylcobalamin riboswitch

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

2012-08-22T05:37:39Z

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

←Older revision

Revision as of 05:37, 22 August 2012

OCA: New page: '''Unreleased structure''' The entry 4gma is ON HOLD Authors: Reyes, F.E., Johnson, J.E., Polaski, J.T., Batey, R.T. Description: Crystal structure of the adenosylcobalamin riboswitch

2012-08-22T05:37:38Z

New page: '''Unreleased structure''' The entry 4gma is ON HOLD Authors: Reyes, F.E., Johnson, J.E., Polaski, J.T., Batey, R.T. Description: Crystal structure of the adenosylcobalamin riboswitch

New page

'''Unreleased structure'''

The entry 4gma is ON HOLD

Authors: Reyes, F.E., Johnson, J.E., Polaski, J.T., Batey, R.T.

Description: Crystal structure of the adenosylcobalamin riboswitch