OCA at 15:23, 18 October 2023

2023-10-18T15:23:32Z

←Older revision		Revision as of 15:23, 18 October 2023
Line 1:		Line 1:

-	====	+	==RNA polymerase II elongation complex with unnatural base dTPT3, rNaMTP bound to E-site==
-	<StructureSection load='7kee' size='340' side='right'caption='[[7kee]]' scene=''>	+	<StructureSection load='7kee' size='340' side='right'caption='[[7kee]], [[Resolution\|resolution]] 3.45Å' 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= OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7kee]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7KEE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7KEE FirstGlance]. <br>
-	</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=7kee FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7kee OCA], [https://pdbe.org/7kee PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7kee RCSB], [https://www.ebi.ac.uk/pdbsum/7kee PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7kee 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]] 3.45Å</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=WC7:6-[2-deoxy-5-O-(trihydroxy-lambda~5~-phosphanyl)-beta-D-erythro-pentofuranosyl]thieno[2,3-c]pyridine-7(6H)-thione'>WC7</scene>, <scene name='pdbligand=WCG:(1S)-1,4-anhydro-5-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-1-(3-methoxynaphthalen-2-yl)-D-ribitol'>WCG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=7kee FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7kee OCA], [https://pdbe.org/7kee PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7kee RCSB], [https://www.ebi.ac.uk/pdbsum/7kee PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7kee ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/RPAB1_YEAST RPAB1_YEAST] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, RPB5 is part of the lower jaw surrounding the central large cleft and thought to grab the incoming DNA template. Seems to be the major component in this process (By similarity).
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The development of unnatural base pairs (UBPs) has greatly increased the information storage capacity of DNA, allowing for transcription of unnatural RNA by the heterologously expressed T7 RNA polymerase (RNAP) in Escherichia coli. However, little is known about how UBPs are transcribed by cellular RNA polymerases. Here, we investigated how synthetic unnatural nucleotides, NaM and TPT3, are recognized by eukaryotic RNA polymerase II (Pol II) and found that Pol II is able to selectively recognize UBPs with high fidelity when dTPT3 is in the template strand and rNaMTP acts as the nucleotide substrate. Our structural analysis and molecular dynamics simulation provide structural insights into transcriptional processing of UBPs in a stepwise manner. Intriguingly, we identified a novel 3'-RNA binding site after rNaM addition, termed the swing state. These results may pave the way for future studies in the design of transcription and translation strategies in higher organisms with expanded genetic codes.
		+
		+	Transcriptional processing of an unnatural base pair by eukaryotic RNA polymerase II.,Oh J, Shin J, Unarta IC, Wang W, Feldman AW, Karadeema RJ, Xu L, Xu J, Chong J, Krishnamurthy R, Huang X, Romesberg FE, Wang D Nat Chem Biol. 2021 Aug;17(8):906-914. doi: 10.1038/s41589-021-00817-3. Epub 2021 , Jun 17. PMID:34140682<ref>PMID:34140682</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7kee" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[RNA polymerase 3D structures\|RNA polymerase 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Z-disk~~]]	+	[[Category: Saccharomyces cerevisiae S288C]]
		+	[[Category: Synthetic construct]]
		+	[[Category: Oh J]]
		+	[[Category: Wang D]]

OCA at 07:32, 25 June 2021

2021-06-25T07:32:18Z

←Older revision		Revision as of 07:32, 25 June 2021
Line 1:		Line 1:
-	'''Unreleased structure'''

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

OCA at 04:14, 28 April 2021

2021-04-28T04:14:05Z

←Older revision		Revision as of 04:14, 28 April 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

OCA at 09:19, 31 March 2021

2021-03-31T09:19:39Z

←Older revision		Revision as of 09:19, 31 March 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7kee is ON HOLD ~~until Paper Publication~~	+	The entry 7kee is ON HOLD

	Authors:		Authors:

OCA at 08:06, 18 November 2020

2020-11-18T08:06:08Z

←Older revision		Revision as of 08:06, 18 November 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

2020-10-21T06:52:22Z

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

←Older revision

Revision as of 06:52, 21 October 2020

OCA: New page: '''Unreleased structure''' The entry 7kee is ON HOLD Authors: Description: Category: Unreleased Structures

2020-10-21T06:52:20Z

New page: '''Unreleased structure''' The entry 7kee is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 7kee is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]