6pln - Revision history

OCA at 14:55, 13 March 2024

OCA — Wed, 13 Mar 2024 14:55:15 GMT

←Older revision		Revision as of 14:55, 13 March 2024
Line 3:		Line 3:
	<StructureSection load='6pln' size='340' side='right'caption='[[6pln]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='6pln' size='340' side='right'caption='[[6pln]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6pln]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_43587 Atcc 43587~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PLN OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6PLN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6pln]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_furiosus Pyrococcus furiosus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PLN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6PLN FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~tfe~~, ~~PF0491 (~~[~~http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=2261 ATCC 43587])~~</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]] 2.6Å</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=6pln FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pln OCA], [~~http~~://pdbe.org/6pln PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6pln RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6pln PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6pln 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=6pln FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pln OCA], [https://pdbe.org/6pln PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6pln RCSB], [https://www.ebi.ac.uk/pdbsum/6pln PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6pln ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/TFE_PYRFU TFE_PYRFU]] Transcription factor that plays a role in the activation of archaeal genes transcribed by RNA polymerase. Facilitates transcription initiation by enhancing TATA-box recognition by TATA-box-binding protein (Tbp), and transcription factor B (Tfb) and RNA polymerase recruitment. Not absolutely required for transcription in vitro, but particularly important in cases where Tbp or Tfb function is not optimal. It dynamically alters the nucleic acid-binding properties of RNA polymerases by stabilizing the initiation complex and destabilizing elongation complexes. Seems to translocate with the RNA polymerase following initiation and acts by binding to the non template strand of the transcription bubble in elongation complexes.<ref>PMID:17921145</ref> <ref>PMID:17965161</ref>	+	[https://www.uniprot.org/uniprot/TFE_PYRFU TFE_PYRFU] Transcription factor that plays a role in the activation of archaeal genes transcribed by RNA polymerase. Facilitates transcription initiation by enhancing TATA-box recognition by TATA-box-binding protein (Tbp), and transcription factor B (Tfb) and RNA polymerase recruitment. Not absolutely required for transcription in vitro, but particularly important in cases where Tbp or Tfb function is not optimal. It dynamically alters the nucleic acid-binding properties of RNA polymerases by stabilizing the initiation complex and destabilizing elongation complexes. Seems to translocate with the RNA polymerase following initiation and acts by binding to the non template strand of the transcription bubble in elongation complexes.<ref>PMID:17921145</ref> <ref>PMID:17965161</ref>
-	~~<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 6pln" style="background-color:#fffaf0;"></div>~~	+
-		+
-	~~==See Also==~~	+
-	*[[Transcription initiation factors 3D structures\|Transcription initiation factors 3D structures]]	+
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 43587]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Jun, S H~~]]	+	[[Category: Pyrococcus furiosus]]
-	[[Category: ~~Murakami, K S~~]]	+	[[Category: Jun SH]]
-	[[Category: ~~General transcription factor]]~~	+	[[Category: Murakami KS]]
-	~~[[Category: Tfe]]~~	+
-	~~[[Category: Transcription~~]]	+

OCA at 05:59, 20 January 2021

OCA — Wed, 20 Jan 2021 05:59:34 GMT

←Older revision		Revision as of 05:59, 20 January 2021
Line 1:		Line 1:

	==X-ray crystal structure of Pyrococcus furiosus general transcription factor TFE-alpha==		==X-ray crystal structure of Pyrococcus furiosus general transcription factor TFE-alpha==
-	<StructureSection load='6pln' size='340' side='right'caption='[[6pln]]' scene=''>	+	<StructureSection load='6pln' size='340' side='right'caption='[[6pln]], [[Resolution\|resolution]] 2.60Å' 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=6PLN OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6PLN FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6pln]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43587 Atcc 43587]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PLN OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6PLN 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=6pln FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pln OCA], [http://pdbe.org/6pln PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pln RCSB], [http://www.ebi.ac.uk/pdbsum/6pln PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pln ProSAT]</span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">tfe, PF0491 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2261 ATCC 43587])</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=6pln FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pln OCA], [http://pdbe.org/6pln PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pln RCSB], [http://www.ebi.ac.uk/pdbsum/6pln PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pln ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/TFE_PYRFU TFE_PYRFU]] Transcription factor that plays a role in the activation of archaeal genes transcribed by RNA polymerase. Facilitates transcription initiation by enhancing TATA-box recognition by TATA-box-binding protein (Tbp), and transcription factor B (Tfb) and RNA polymerase recruitment. Not absolutely required for transcription in vitro, but particularly important in cases where Tbp or Tfb function is not optimal. It dynamically alters the nucleic acid-binding properties of RNA polymerases by stabilizing the initiation complex and destabilizing elongation complexes. Seems to translocate with the RNA polymerase following initiation and acts by binding to the non template strand of the transcription bubble in elongation complexes.<ref>PMID:17921145</ref> <ref>PMID:17965161</ref>
		+	<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 6pln" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Transcription initiation factors 3D structures\|Transcription initiation factors 3D structures]]
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 43587]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Jun SH]]	+	[[Category: Jun, S H]]
-	[[Category: Murakami KS]]	+	[[Category: Murakami, K S]]
		+	[[Category: General transcription factor]]
		+	[[Category: Tfe]]
		+	[[Category: Transcription]]

OCA at 14:01, 8 July 2020

OCA — Wed, 08 Jul 2020 14:01:11 GMT

←Older revision		Revision as of 14:01, 8 July 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 6pln is ON HOLD until Paper Publication~~	+	==X-ray crystal structure of Pyrococcus furiosus general transcription factor TFE-alpha==
-		+	<StructureSection load='6pln' size='340' side='right'caption='[[6pln]]' scene=''>
-	~~Authors: Murakami, K.S., Jun, S.H.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PLN OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6PLN FirstGlance]. <br>
-	~~Description:~~ X-ray crystal structure of Pyrococcus furiosus general transcription factor TFE-alpha	+	</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=6pln FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pln OCA], [http://pdbe.org/6pln PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pln RCSB], [http://www.ebi.ac.uk/pdbsum/6pln PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pln ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[~~Category~~: ~~Murakami~~, K.S]]	+	__TOC__
-	[[Category: Jun~~, S.H~~]]	+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Jun SH]]
		+	[[Category: Murakami KS]]

OCA at 04:12, 21 August 2019

OCA — Wed, 21 Aug 2019 04:12:44 GMT

←Older revision		Revision as of 04:12, 21 August 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Murakami, K.S., Jun, S.H.		Authors: Murakami, K.S., Jun, S.H.

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

OCA — Wed, 10 Jul 2019 04:14:14 GMT

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

←Older revision

Revision as of 04:14, 10 July 2019

OCA: New page: '''Unreleased structure''' The entry 6pln is ON HOLD Authors: Murakami, K.S., Jun, S.H. Description: X-ray crystal structure of Pyrococcus furiosus general transcription factor TFE-alp...

OCA — Wed, 10 Jul 2019 04:14:12 GMT

New page: '''Unreleased structure''' The entry 6pln is ON HOLD Authors: Murakami, K.S., Jun, S.H. Description: X-ray crystal structure of Pyrococcus furiosus general transcription factor TFE-alp...

New page

'''Unreleased structure'''

The entry 6pln is ON HOLD

Authors: Murakami, K.S., Jun, S.H.

Description: X-ray crystal structure of Pyrococcus furiosus general transcription factor TFE-alpha
[[Category: Unreleased Structures]]
[[Category: Murakami, K.S]]
[[Category: Jun, S.H]]