8dh4 - Revision history

OCA at 10:09, 25 October 2023

2023-10-25T10:09:44Z

←Older revision		Revision as of 10:09, 25 October 2023
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[8dh4]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_phage_T7 Escherichia phage T7] 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=8DH4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8DH4 FirstGlance]. <br>		<table><tr><td colspan='2'>[[8dh4]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_phage_T7 Escherichia phage T7] 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=8DH4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8DH4 FirstGlance]. <br>
-	</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=S8U:1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-1H-pyrrole-2-carbaldehyde'>S8U</scene>, <scene name='pdbligand=S96:(7P)-3-{5-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-ribofuranosyl}-7-(thiophen-2-yl)-3H-imidazo[4,5-b]pyridine'>S96</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]] 2.8Å</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=S8U:1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-1H-pyrrole-2-carbaldehyde'>S8U</scene>, <scene name='pdbligand=S96:(7P)-3-{5-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-ribofuranosyl}-7-(thiophen-2-yl)-3H-imidazo[4,5-b]pyridine'>S96</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=8dh4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8dh4 OCA], [https://pdbe.org/8dh4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8dh4 RCSB], [https://www.ebi.ac.uk/pdbsum/8dh4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8dh4 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=8dh4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8dh4 OCA], [https://pdbe.org/8dh4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8dh4 RCSB], [https://www.ebi.ac.uk/pdbsum/8dh4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8dh4 ProSAT]</span></td></tr>
	</table>		</table>

OCA at 11:21, 1 February 2023

2023-02-01T11:21:22Z

←Older revision		Revision as of 11:21, 1 February 2023
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-	'''Unreleased structure'''

-	~~The entry~~ 8dh4 is ~~ON HOLD until Paper~~ Publication	+	==T7 RNA polymerase elongation complex with unnatural base dPa-DsTP pair==
		+	<StructureSection load='8dh4' size='340' side='right'caption='[[8dh4]], [[Resolution\|resolution]] 2.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[8dh4]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_phage_T7 Escherichia phage T7] 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=8DH4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8DH4 FirstGlance]. <br>
		+	</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=S8U:1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-1H-pyrrole-2-carbaldehyde'>S8U</scene>, <scene name='pdbligand=S96:(7P)-3-{5-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-ribofuranosyl}-7-(thiophen-2-yl)-3H-imidazo[4,5-b]pyridine'>S96</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=8dh4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8dh4 OCA], [https://pdbe.org/8dh4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8dh4 RCSB], [https://www.ebi.ac.uk/pdbsum/8dh4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8dh4 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/RPOL_BPT7 RPOL_BPT7] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Responsible for the transcription of the late genes of T7. It is rifampicin-resistant. It recognizes a specific promoter sequence, unwinds the double-stranded RNA to expose the coding strand for templating, initiates transcription preferentially with a purine.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Bacteriophage T7 RNA polymerase (T7 RNAP) is widely used for synthesizing RNA molecules with synthetic modifications and unnatural base pairs (UBPs) for a variety of biotechnical and therapeutic applications. However, the molecular basis of transcription recognition of UBPs by T7 RNAP remains poorly understood. Here we focused on a representative UBP, 7-(2-thienyl)-imidazo[4,5-b]pyridine (Ds) and pyrrole 2-carbaldehyde (Pa), and investigated how the hydrophobic Ds-Pa pair is recognized by T7 RNAP. Our kinetic assays revealed that T7 RNAP selectively recognizes the Ds or Pa base in the templates and preferentially incorporates their cognate unnatural base nucleotide substrate (PaTP or DsTP) over natural NTPs. Our structural studies reveal that T7 RNAP recognizes the unnatural substrates at the pre-insertion state in a distinct manner compared to natural substrates. These results provide mechanistic insights into transcription recognition of UBP by T7 RNAP and provide valuable information for designing the next generation of UBPs.

-	~~Authors~~:	+	Structural basis of transcription recognition of a hydrophobic unnatural base pair by T7 RNA polymerase.,Oh J, Kimoto M, Xu H, Chong J, Hirao I, Wang D Nat Commun. 2023 Jan 13;14(1):195. doi: 10.1038/s41467-022-35755-8. PMID:36635281<ref>PMID:36635281</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 8dh4" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Escherichia phage T7]]
		+	[[Category: Large Structures]]
		+	[[Category: Synthetic construct]]
		+	[[Category: Oh J]]
		+	[[Category: Wang D]]

OCA at 03:52, 3 August 2022

2022-08-03T03:52:47Z

←Older revision		Revision as of 03:52, 3 August 2022
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 8dh4 is ON HOLD	+	The entry 8dh4 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "8dh4" [edit=sysop:move=sysop]

2022-07-06T15:13:09Z

Protected "8dh4" [edit=sysop:move=sysop]

←Older revision

Revision as of 15:13, 6 July 2022

OCA: New page: '''Unreleased structure''' The entry 8dh4 is ON HOLD Authors: Description: Category: Unreleased Structures

2022-07-06T15:13:08Z

New page: '''Unreleased structure''' The entry 8dh4 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 8dh4 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]