OCA at 11:30, 24 January 2024

OCA — Wed, 24 Jan 2024 11:30:27 GMT

←Older revision		Revision as of 11:30, 24 January 2024
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-	'''Unreleased structure'''

-	~~The entry~~ 8tvp is ~~ON HOLD until 2025~~-08-18	+	==Cryo-EM structure of CPD-stalled Pol II in complex with Rad26 (open state)==
		+	<StructureSection load='8tvp' size='340' side='right'caption='[[8tvp]], [[Resolution\|resolution]] 3.70Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[8tvp]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8TVP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8TVP FirstGlance]. <br>
		+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution\|Resolution]] 3.7Å</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=TTD:CIS-SYN+CYCLOBUTANE+THYMINE+DIMER'>TTD</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=8tvp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8tvp OCA], [https://pdbe.org/8tvp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8tvp RCSB], [https://www.ebi.ac.uk/pdbsum/8tvp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8tvp ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/RPB1_YEAST RPB1_YEAST] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Largest and catalytic component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Forms the polymerase active center together with the second largest subunit. Pol II is the central component of the basal RNA polymerase II transcription machinery. During a transcription cycle, Pol II, general transcription factors and the Mediator complex assemble as the preinitiation complex (PIC) at the promoter. 11-15 base pairs of DNA surrounding the transcription start site are melted and the single stranded DNA template strand of the promoter is positioned deeply within the central active site cleft of Pol II to form the open complex. After synthesis of about 30 bases of RNA, Pol II releases its contacts with the core promoter and the rest of the transcription machinery (promoter clearance) and enters the stage of transcription elongation in which it moves on the template as the transcript elongates. Pol II appears to oscillate between inactive and active conformations at each step of nucleotide addition. Elongation is influenced by the phosphorylation status of the C-terminal domain (CTD) of Pol II largest subunit (RPB1), which serves as a platform for assembly of factors that regulate transcription initiation, elongation, termination and mRNA processing. Pol II is composed of mobile elements that move relative to each other. The core element with the central large cleft comprises RPB3, RBP10, RPB11, RPB12 and regions of RPB1 and RPB2 forming the active center. The clamp element (portions of RPB1, RPB2 and RPB3) is connected to the core through a set of flexible switches and moves to open and close the cleft. A bridging helix emanates from RPB1 and crosses the cleft near the catalytic site and is thought to promote translocation of Pol II by acting as a ratchet that moves the RNA-DNA hybrid through the active site by switching from straight to bent conformations at each step of nucleotide addition. In elongating Pol II, the lid loop (RPB1) appears to act as a wedge to drive apart the DNA and RNA strands at the upstream end of the transcription bubble and guide the RNA strand toward the RNA exit groove located near the base of the largely unstructured CTD domain of RPB1. The rudder loop (RPB1) interacts with single stranded DNA after separation from the RNA strand, likely preventing reassociation with the exiting RNA. The cleft is surrounded by jaws: an upper jaw formed by portions of RBP1, RPB2 and RPB9, and a lower jaw, formed by RPB5 and portions of RBP1. The jaws are thought to grab the incoming DNA template, mainly by RPB5 direct contacts to DNA.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Transcription-coupled nucleotide excision repair (TC-NER) is a highly conserved DNA repair pathway that removes bulky lesions in the transcribed genome. Cockayne syndrome B protein (CSB), or its yeast ortholog Rad26, has been known for decades to play important roles in the lesion-recognition steps of TC-NER. Another conserved protein ELOF1, or its yeast ortholog Elf1, was recently identified as a core transcription-coupled repair factor. How Rad26 distinguishes between RNA polymerase II (Pol II) stalled at a DNA lesion or other obstacles and what role Elf1 plays in this process remains unknown. Here, we present cryo-EM structures of Pol II-Rad26 complexes stalled at different obstacles that show that Rad26 uses a common mechanism to recognize a stalled Pol II, with additional interactions when Pol II is arrested at a lesion. A cryo-EM structure of lesion-arrested Pol II-Rad26 bound to Elf1 revealed that Elf1 induces further interactions between Rad26 and a lesion-arrested Pol II. Biochemical and genetic data support the importance of the interplay between Elf1 and Rad26 in TC-NER initiation. Together, our results provide important mechanistic insights into how two conserved transcription-coupled repair factors, Rad26/CSB and Elf1/ELOF1, work together at the initial lesion recognition steps of transcription-coupled repair.

-	~~Authors~~:	+	Elf1 promotes Rad26's interaction with lesion-arrested Pol II for transcription-coupled repair.,Sarsam RD, Xu J, Lahiri I, Gong W, Li Q, Oh J, Zhou Z, Hou P, Chong J, Hao N, Li S, Wang D, Leschziner AE Proc Natl Acad Sci U S A. 2024 Jan 16;121(3):e2314245121. doi: , 10.1073/pnas.2314245121. Epub 2024 Jan 9. PMID:38194460<ref>PMID:38194460</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 8tvp" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Saccharomyces cerevisiae]]
		+	[[Category: Lahiri I]]
		+	[[Category: Leschziner AE]]
		+	[[Category: Sarsam RD]]

OCA at 10:06, 3 January 2024

OCA — Wed, 03 Jan 2024 10:06:52 GMT

←Older revision		Revision as of 10:06, 3 January 2024
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 8tvp is ON HOLD	+	The entry 8tvp is ON HOLD until 2025-08-18

	Authors:		Authors:

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

OCA — Wed, 30 Aug 2023 07:44:18 GMT

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

←Older revision

Revision as of 07:44, 30 August 2023

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

OCA — Wed, 30 Aug 2023 07:44:17 GMT

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

New page

'''Unreleased structure'''

The entry 8tvp is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]

8tvp - Revision history

OCA at 11:30, 24 January 2024

OCA at 10:06, 3 January 2024

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

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