6ymw - Revision history

OCA at 15:01, 18 October 2023

OCA — Wed, 18 Oct 2023 15:01:39 GMT

←Older revision		Revision as of 15:01, 18 October 2023
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-	====	+	==Cryo-EM structure of yeast mitochondrial RNA polymerase transcription initiation complex==
-	<StructureSection load='6ymw' size='340' side='right'caption='[[6ymw]]' scene=''>	+	<StructureSection load='6ymw' size='340' side='right'caption='[[6ymw]], [[Resolution\|resolution]] 3.71Å' 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'>[[6ymw]] is a 5 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=6YMW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YMW 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=6ymw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ymw OCA], [https://pdbe.org/6ymw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ymw RCSB], [https://www.ebi.ac.uk/pdbsum/6ymw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ymw ProSAT]</span></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution\|Resolution]] 3.71Å</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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=P5E:[[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-sulfanyl-phosphoryl]+phosphono+hydrogen+phosphate'>P5E</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=6ymw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ymw OCA], [https://pdbe.org/6ymw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ymw RCSB], [https://www.ebi.ac.uk/pdbsum/6ymw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ymw ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/MTF1_YEAST MTF1_YEAST] Mitochondrial transcription factor that confers selective promoter recognition on the core subunit of the yeast mitochondrial RNA polymerase. Interacts with DNA in a non-specific manner.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Mitochondrial RNA polymerase (mtRNAP) is crucial in cellular energy production, yet understanding of mitochondrial DNA transcription initiation lags that of bacterial and nuclear DNA transcription. We report structures of two transcription initiation intermediate states of yeast mtRNAP that explain promoter melting, template alignment, DNA scrunching, abortive synthesis, and transition into elongation. In the partially melted initiation complex (PmIC), transcription factor MTF1 makes base-specific interactions with flipped non-template (NT) nucleotides "AAGT" at -4 to -1 positions of the DNA promoter. In the initiation complex (IC), the template in the expanded 7-mer bubble positions the RNA and NTP analog UTPalphaS, while NT scrunches into an NT loop. The scrunched NT loop is stabilized by the centrally positioned MTF1 C-tail. The IC and PmIC states coexist in solution, revealing a dynamic equilibrium between two functional states. Frequent scrunching/unscruching transitions and the imminent steric clashes of the inflating NT loop and growing RNA:DNA with the C-tail explain abortive synthesis and transition into elongation.
		+
		+	Cryo-EM Structures Reveal Transcription Initiation Steps by Yeast Mitochondrial RNA Polymerase.,De Wijngaert B, Sultana S, Singh A, Dharia C, Vanbuel H, Shen J, Vasilchuk D, Martinez SE, Kandiah E, Patel SS, Das K Mol Cell. 2021 Jan 21;81(2):268-280.e5. doi: 10.1016/j.molcel.2020.11.016. Epub , 2020 Dec 4. PMID:33278362<ref>PMID:33278362</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6ymw" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Z-disk~~]]	+	[[Category: Saccharomyces cerevisiae S288C]]
		+	[[Category: Synthetic construct]]
		+	[[Category: Das K]]
		+	[[Category: Patel SS]]

OCA at 11:17, 3 February 2021

OCA — Wed, 03 Feb 2021 11:17:03 GMT

←Older revision		Revision as of 11:17, 3 February 2021
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	<StructureSection load='6ymw' size='340' side='right'caption='[[6ymw]]' scene=''>		<StructureSection load='6ymw' size='340' side='right'caption='[[6ymw]]' 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 [~~http~~://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>	+	<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>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6ymw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ymw OCA], [~~http~~://pdbe.org/6ymw PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6ymw RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6ymw PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6ymw ProSAT]</span></td></tr>	+	</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=6ymw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ymw OCA], [https://pdbe.org/6ymw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ymw RCSB], [https://www.ebi.ac.uk/pdbsum/6ymw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ymw ProSAT]</span></td></tr>
	</table>		</table>
	__TOC__		__TOC__

OCA at 06:37, 9 December 2020

OCA — Wed, 09 Dec 2020 06:37:42 GMT

←Older revision		Revision as of 06:37, 9 December 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 6ymw ~~is ON HOLD until Paper Publication~~	+	====
-		+	<StructureSection load='6ymw' size='340' side='right'caption='[[6ymw]]' scene=''>
-	~~Authors~~: ~~Das, K~~.~~, Patel, S~~.S.	+	== 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 [http://proteopedia.org/fgij/fg.htm?mol= FirstGlance]. <br>
-	~~Description: Cryo~~-EM structure ~~of yeast mitochondrial RNA polymerase transcription initiation complex~~	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6ymw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ymw OCA], [http://pdbe.org/6ymw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ymw RCSB], [http://www.ebi.ac.uk/pdbsum/6ymw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ymw ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[~~Category~~: ~~Patel~~, S.S]]	+	__TOC__
-	[[Category: ~~Das, K~~]]	+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Z-disk]]

OCA at 18:48, 28 October 2020

OCA — Wed, 28 Oct 2020 18:48:29 GMT

←Older revision		Revision as of 18:48, 28 October 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6ymw is ON HOLD	+	The entry 6ymw is ON HOLD until Paper Publication

	Authors: Das, K., Patel, S.S.		Authors: Das, K., Patel, S.S.

OCA at 04:20, 7 October 2020

OCA — Wed, 07 Oct 2020 04:20:00 GMT

←Older revision		Revision as of 04:20, 7 October 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6ymw is ON HOLD ~~until Paper Publication~~	+	The entry 6ymw is ON HOLD

	Authors: Das, K., Patel, S.S.		Authors: Das, K., Patel, S.S.
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	Description: Cryo-EM structure of yeast mitochondrial RNA polymerase transcription initiation complex		Description: Cryo-EM structure of yeast mitochondrial RNA polymerase transcription initiation complex
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Das, K]]
	[[Category: Patel, S.S]]		[[Category: Patel, S.S]]
		+	[[Category: Das, K]]

OCA at 07:28, 22 July 2020

OCA — Wed, 22 Jul 2020 07:28:58 GMT

←Older revision		Revision as of 07:28, 22 July 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6ymw is ON HOLD	+	The entry 6ymw is ON HOLD until Paper Publication

	Authors: Das, K., Patel, S.S.		Authors: Das, K., Patel, S.S.
Line 7:		Line 7:
	Description: Cryo-EM structure of yeast mitochondrial RNA polymerase transcription initiation complex		Description: Cryo-EM structure of yeast mitochondrial RNA polymerase transcription initiation complex
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Patel, S.S]]
	[[Category: Das, K]]		[[Category: Das, K]]
		+	[[Category: Patel, S.S]]

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

OCA — Wed, 15 Apr 2020 05:39:01 GMT

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

←Older revision

Revision as of 05:39, 15 April 2020

OCA: New page: '''Unreleased structure''' The entry 6ymw is ON HOLD Authors: Das, K., Patel, S.S. Description: Cryo-EM structure of yeast mitochondrial RNA polymerase transcription initiation complex...

OCA — Wed, 15 Apr 2020 05:39:00 GMT

New page: '''Unreleased structure''' The entry 6ymw is ON HOLD Authors: Das, K., Patel, S.S. Description: Cryo-EM structure of yeast mitochondrial RNA polymerase transcription initiation complex...

New page

'''Unreleased structure'''

The entry 6ymw is ON HOLD

Authors: Das, K., Patel, S.S.

Description: Cryo-EM structure of yeast mitochondrial RNA polymerase transcription initiation complex
[[Category: Unreleased Structures]]
[[Category: Patel, S.S]]
[[Category: Das, K]]