6kf9 - Revision history

OCA at 19:27, 29 May 2024

OCA — Wed, 29 May 2024 19:27:26 GMT

←Older revision		Revision as of 19:27, 29 May 2024
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-	====	+	==Cryo-EM structure of Thermococcus kodakarensis RNA polymerase==
-	<StructureSection load='6kf9' size='340' side='right'caption='[[6kf9]]' scene=''>	+	<StructureSection load='6kf9' size='340' side='right'caption='[[6kf9]], [[Resolution\|resolution]] 3.79Å' 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'>[[6kf9]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermococcus_kodakarensis_KOD1 Thermococcus kodakarensis KOD1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KF9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6KF9 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=6kf9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kf9 OCA], [https://pdbe.org/6kf9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6kf9 RCSB], [https://www.ebi.ac.uk/pdbsum/6kf9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6kf9 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]] 3.79Å</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=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=6kf9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kf9 OCA], [https://pdbe.org/6kf9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6kf9 RCSB], [https://www.ebi.ac.uk/pdbsum/6kf9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6kf9 ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q5JE33_THEKO Q5JE33_THEKO]
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Opening of the DNA binding cleft of cellular RNA polymerase (RNAP) is necessary for transcription initiation but the underlying molecular mechanism is not known. Here, we report on the cryo-electron microscopy structures of the RNAP, RNAP-TFEalpha binary, and RNAP-TFEalpha-promoter DNA ternary complexes from archaea, Thermococcus kodakarensis (Tko). The structures reveal that TFEalpha bridges the RNAP clamp and stalk domains to open the DNA binding cleft. Positioning of promoter DNA into the cleft closes it while maintaining the TFEalpha interactions with the RNAP mobile modules. The structures and photo-crosslinking results also suggest that the conserved aromatic residue in the extended winged-helix domain of TFEalpha interacts with promoter DNA to stabilize the transcription bubble. This study provides a structural basis for the functions of TFEalpha and elucidates the mechanism by which the DNA binding cleft is opened during transcription initiation in the stalk-containing RNAPs, including archaeal and eukaryotic RNAPs.
		+
		+	Direct binding of TFEalpha opens DNA binding cleft of RNA polymerase.,Jun SH, Hyun J, Cha JS, Kim H, Bartlett MS, Cho HS, Murakami KS Nat Commun. 2020 Nov 30;11(1):6123. doi: 10.1038/s41467-020-19998-x. PMID:33257704<ref>PMID:33257704</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6kf9" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[RNA polymerase 3D structures\|RNA polymerase 3D structures]]
		+	*[[Transcription initiation factors 3D structures\|Transcription initiation factors 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Z-~~disk~~]]	+	[[Category: Thermococcus kodakarensis KOD1]]
		+	[[Category: Bartlett MS]]
		+	[[Category: Cha JS]]
		+	[[Category: Cho H-S]]
		+	[[Category: Hyun J]]
		+	[[Category: Jeong H]]
		+	[[Category: Jun S-H]]
		+	[[Category: Kim H]]
		+	[[Category: Murakami KS]]

OCA at 08:48, 18 February 2021

OCA — Thu, 18 Feb 2021 08:48:25 GMT

←Older revision		Revision as of 08:48, 18 February 2021
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	<StructureSection load='6kf9' size='340' side='right'caption='[[6kf9]]' scene=''>		<StructureSection load='6kf9' size='340' side='right'caption='[[6kf9]]' 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=6kf9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kf9 OCA], [~~http~~://pdbe.org/6kf9 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6kf9 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6kf9 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6kf9 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=6kf9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kf9 OCA], [https://pdbe.org/6kf9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6kf9 RCSB], [https://www.ebi.ac.uk/pdbsum/6kf9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6kf9 ProSAT]</span></td></tr>
	</table>		</table>
	__TOC__		__TOC__

OCA at 10:47, 24 December 2020

OCA — Thu, 24 Dec 2020 10:47:50 GMT

←Older revision		Revision as of 10:47, 24 December 2020
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-	'''Unreleased structure'''

-	~~The entry~~ 6kf9 ~~is ON HOLD until Paper Publication~~	+	====
-		+	<StructureSection load='6kf9' size='340' side='right'caption='[[6kf9]]' scene=''>
-	~~Authors~~: ~~Jun, S~~.-H.~~, Hyun, J~~.~~, Jeong, H~~.~~, Cha, J~~.S.~~, Kim, H~~.~~, Bartlett, M~~.S., ~~Cho, H~~.-S.~~, Murakami, K~~.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 Thermococcus kodakarensis RNA polymerase~~	+	</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=6kf9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kf9 OCA], [http://pdbe.org/6kf9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6kf9 RCSB], [http://www.ebi.ac.uk/pdbsum/6kf9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6kf9 ProSAT]</span></td></tr>
-	~~[[Category: Unreleased Structures~~]]	+	</table>
-	~~[[Category: Kim~~, ~~H]]~~	+	__TOC__
-	[~~[Category~~: ~~Murakami, K~~.S]]	+	</StructureSection>
-	~~[[Category: Hyun~~, ~~J]]~~	+	[[Category: Large Structures]]
-	[~~[Category~~: ~~Bartlett, M~~.S]]	+	[[Category: Z-disk]]
-	[~~[Category~~: ~~Cha, J~~.S]]	+
-	[~~[Category~~: ~~Cho, H~~.-S]]	+
-	[[Category: ~~Jun, S.-H~~]]	+
-	[[Category: ~~Jeong, H~~]]	+

OCA at 14:53, 14 August 2019

OCA — Wed, 14 Aug 2019 14:53:35 GMT

←Older revision		Revision as of 14:53, 14 August 2019
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6kf9 is ON HOLD	+	The entry 6kf9 is ON HOLD until Paper Publication

	Authors: Jun, S.-H., Hyun, J., Jeong, H., Cha, J.S., Kim, H., Bartlett, M.S., Cho, H.-S., Murakami, K.S.		Authors: Jun, S.-H., Hyun, J., Jeong, H., Cha, J.S., Kim, H., Bartlett, M.S., Cho, H.-S., Murakami, K.S.
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	[[Category: Kim, H]]		[[Category: Kim, H]]
	[[Category: Murakami, K.S]]		[[Category: Murakami, K.S]]
-	[[Category: Bartlett, M.S]]
	[[Category: Hyun, J]]		[[Category: Hyun, J]]
-	[[Category: ~~Cho~~, H.-S]]	+	[[Category: Bartlett, M.S]]
	[[Category: Cha, J.S]]		[[Category: Cha, J.S]]
		+	[[Category: Cho, H.-S]]
	[[Category: Jun, S.-H]]		[[Category: Jun, S.-H]]
	[[Category: Jeong, H]]		[[Category: Jeong, H]]

OCA: Protected "6kf9" [edit=sysop:move=sysop]

OCA — Wed, 17 Jul 2019 08:43:42 GMT

Protected "6kf9" [edit=sysop:move=sysop]

←Older revision

Revision as of 08:43, 17 July 2019

OCA: New page: '''Unreleased structure''' The entry 6kf9 is ON HOLD Authors: Jun, S.-H., Hyun, J., Jeong, H., Cha, J.S., Kim, H., Bartlett, M.S., Cho, H.-S., Murakami, K.S. Description: Cryo-EM struc...

OCA — Wed, 17 Jul 2019 08:43:41 GMT

New page: '''Unreleased structure''' The entry 6kf9 is ON HOLD Authors: Jun, S.-H., Hyun, J., Jeong, H., Cha, J.S., Kim, H., Bartlett, M.S., Cho, H.-S., Murakami, K.S. Description: Cryo-EM struc...

New page

'''Unreleased structure'''

The entry 6kf9 is ON HOLD

Authors: Jun, S.-H., Hyun, J., Jeong, H., Cha, J.S., Kim, H., Bartlett, M.S., Cho, H.-S., Murakami, K.S.

Description: Cryo-EM structure of Thermococcus kodakarensis RNA polymerase
[[Category: Unreleased Structures]]
[[Category: Kim, H]]
[[Category: Murakami, K.S]]
[[Category: Bartlett, M.S]]
[[Category: Hyun, J]]
[[Category: Cho, H.-S]]
[[Category: Cha, J.S]]
[[Category: Jun, S.-H]]
[[Category: Jeong, H]]