6dt8 - Revision history

OCA at 14:36, 13 March 2024

OCA — Wed, 13 Mar 2024 14:36:38 GMT

←Older revision		Revision as of 14:36, 13 March 2024
Line 3:		Line 3:
	<StructureSection load='6dt8' size='340' side='right'caption='[[6dt8]], [[Resolution\|resolution]] 3.20Å' scene=''>		<StructureSection load='6dt8' size='340' side='right'caption='[[6dt8]], [[Resolution\|resolution]] 3.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6dt8]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Bpn4 Bpn4~~]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=6c2l 6c2l]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DT8 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca.weizmann.ac~~.~~il/oca-docs~~/fgij/fg.htm?mol=6DT8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6dt8]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_N4 Escherichia virus N4] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=6c2l 6c2l]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DT8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6DT8 FirstGlance]. <br>
-	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6dt8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dt8 OCA], [~~http~~://pdbe.org/6dt8 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6dt8 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6dt8 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6dt8 ProSAT]</span></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]] 3.2Å</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=6dt8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dt8 OCA], [https://pdbe.org/6dt8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6dt8 RCSB], [https://www.ebi.ac.uk/pdbsum/6dt8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6dt8 ProSAT]</span></td></tr>
	</table>		</table>
-	~~<div style~~=~~"background-color:#fffaf0;">~~	+	== Function ==
-	=~~= Publication Abstract from PubMed~~ ==	+	[https://www.uniprot.org/uniprot/Q8LTE4_BPN4 Q8LTE4_BPN4]
-	Genomes of phages, mitochondria, and chloroplasts are transcribed by a diverse group of transcriptional machineries with structurally related single-subunit RNA polymerases (RNAPs). Our understanding of transcription mechanisms of these enzymes is predominantly based on biochemical and structural studies of three most-studied members, transcription factor-independent phage T7 RNAP, transcription factor-dependent phage N4 virion-encapsidated RNAP, and transcription factor-dependent mitochondrial RNAPs (mtRNAP). Although these RNAPs employ completely different mechanisms for promoter recognition and transcription termination, these enzymes are relatively large and formed by single polypeptides. Historically being a model enzyme for studying the mechanisms of transcription by T7-like RNAPs, however, T7 RNAP represents only a small group of RNAPs in this family. The vast majority of T7-like RNAPs are transcription factor-dependent, and several of them are heterodimeric enzymes. Here, we report X-ray crystal structures of transcription complexes of the smallest and heterodimeric form of T7-like RNAP, bacteriophage N4 RNAPII, providing insights into the structural organization of a minimum RNAP in this family. We analyze structural and functional aspects of heterodimeric architecture of N4 RNAPII concerning the mechanisms of transcription initiation and transition to processive RNA elongation. Interestingly, N4 RNAPII maintains the same conformation in promoter-bound and elongation transcription complexes, revealing a novel transcription mechanism for single-subunit RNAPs. This work establishes a structural basis for studying mechanistic aspects of transcription by factor-dependent minimum RNAP.	+
-		+
-	~~Minimalism and functionality~~: ~~Structural lessons from the heterodimeric N4 bacteriophage RNA polymerase II.,Molodtsov V, Murakami KS J Biol Chem. 2018 Aug 31;293(35):13616-13625. doi: 10.1074~~/~~jbc.RA118.003447. Epub, 2018 Jul 10. PMID:29991593<ref>PMID:29991593<~~/~~ref>~~	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U~~.S. ~~National Library of Medicine.<br>~~	+
-	</~~div>~~	+
-	~~<div class="pdbe-citations 6dt8" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references~~/>	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bpn4~~]]	+	[[Category: Escherichia virus N4]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Molodtsov, V~~]]	+	[[Category: Synthetic construct]]
-	[[Category: ~~Murakami, K S~~]]	+	[[Category: Molodtsov V]]
-	[[Category: ~~Bacteriophage]]~~	+	[[Category: Murakami KS]]
-	~~[[Category: N4]]~~	+
-	~~[[Category: Rna polymerase]]~~	+
-	~~[[Category: Transcription]]~~	+
-	~~[[Category: Transcription-dna-rna complex~~]]	+

OCA at 11:08, 1 January 2020

OCA — Wed, 01 Jan 2020 11:08:37 GMT

←Older revision		Revision as of 11:08, 1 January 2020
Line 1:		Line 1:

	==Bacteriophage N4 RNA polymerase II elongation complex 1==		==Bacteriophage N4 RNA polymerase II elongation complex 1==
-	<StructureSection load='6dt8' size='340' side='right' caption='[[6dt8]], [[Resolution\|resolution]] 3.20Å' scene=''>	+	<StructureSection load='6dt8' size='340' side='right'caption='[[6dt8]], [[Resolution\|resolution]] 3.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6dt8]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpn4 Bpn4]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=6c2l 6c2l]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DT8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DT8 FirstGlance]. <br>		<table><tr><td colspan='2'>[[6dt8]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpn4 Bpn4]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=6c2l 6c2l]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DT8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DT8 FirstGlance]. <br>
Line 20:		Line 20:
	</StructureSection>		</StructureSection>
	[[Category: Bpn4]]		[[Category: Bpn4]]
		+	[[Category: Large Structures]]
	[[Category: Molodtsov, V]]		[[Category: Molodtsov, V]]
	[[Category: Murakami, K S]]		[[Category: Murakami, K S]]

OCA at 07:35, 3 October 2018

OCA — Wed, 03 Oct 2018 07:35:07 GMT

←Older revision		Revision as of 07:35, 3 October 2018
Line 3:		Line 3:
	<StructureSection load='6dt8' size='340' side='right' caption='[[6dt8]], [[Resolution\|resolution]] 3.20Å' scene=''>		<StructureSection load='6dt8' size='340' side='right' caption='[[6dt8]], [[Resolution\|resolution]] 3.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6dt8]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DT8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DT8 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6dt8]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpn4 Bpn4]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=6c2l 6c2l]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DT8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DT8 FirstGlance]. <br>
	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6dt8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dt8 OCA], [http://pdbe.org/6dt8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dt8 RCSB], [http://www.ebi.ac.uk/pdbsum/6dt8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dt8 ProSAT]</span></td></tr>		</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6dt8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dt8 OCA], [http://pdbe.org/6dt8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dt8 RCSB], [http://www.ebi.ac.uk/pdbsum/6dt8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dt8 ProSAT]</span></td></tr>
	</table>		</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Genomes of phages, mitochondria, and chloroplasts are transcribed by a diverse group of transcriptional machineries with structurally related single-subunit RNA polymerases (RNAPs). Our understanding of transcription mechanisms of these enzymes is predominantly based on biochemical and structural studies of three most-studied members, transcription factor-independent phage T7 RNAP, transcription factor-dependent phage N4 virion-encapsidated RNAP, and transcription factor-dependent mitochondrial RNAPs (mtRNAP). Although these RNAPs employ completely different mechanisms for promoter recognition and transcription termination, these enzymes are relatively large and formed by single polypeptides. Historically being a model enzyme for studying the mechanisms of transcription by T7-like RNAPs, however, T7 RNAP represents only a small group of RNAPs in this family. The vast majority of T7-like RNAPs are transcription factor-dependent, and several of them are heterodimeric enzymes. Here, we report X-ray crystal structures of transcription complexes of the smallest and heterodimeric form of T7-like RNAP, bacteriophage N4 RNAPII, providing insights into the structural organization of a minimum RNAP in this family. We analyze structural and functional aspects of heterodimeric architecture of N4 RNAPII concerning the mechanisms of transcription initiation and transition to processive RNA elongation. Interestingly, N4 RNAPII maintains the same conformation in promoter-bound and elongation transcription complexes, revealing a novel transcription mechanism for single-subunit RNAPs. This work establishes a structural basis for studying mechanistic aspects of transcription by factor-dependent minimum RNAP.
		+
		+	Minimalism and functionality: Structural lessons from the heterodimeric N4 bacteriophage RNA polymerase II.,Molodtsov V, Murakami KS J Biol Chem. 2018 Aug 31;293(35):13616-13625. doi: 10.1074/jbc.RA118.003447. Epub, 2018 Jul 10. PMID:29991593<ref>PMID:29991593</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6dt8" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bpn4]]
	[[Category: Molodtsov, V]]		[[Category: Molodtsov, V]]
	[[Category: Murakami, K S]]		[[Category: Murakami, K S]]

OCA at 05:45, 11 July 2018

OCA — Wed, 11 Jul 2018 05:45:12 GMT

←Older revision		Revision as of 05:45, 11 July 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 6dt8 is ON HOLD~~	+	==Bacteriophage N4 RNA polymerase II elongation complex 1==
-		+	<StructureSection load='6dt8' size='340' side='right' caption='[[6dt8]], [[Resolution\|resolution]] 3.20Å' scene=''>
-	~~Authors: Molodtsov, V., Murakami, K.S.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6dt8]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6DT8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6DT8 FirstGlance]. <br>
-	~~Description:~~ Bacteriophage N4 RNA polymerase II elongation complex 1	+	</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6dt8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6dt8 OCA], [http://pdbe.org/6dt8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6dt8 RCSB], [http://www.ebi.ac.uk/pdbsum/6dt8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6dt8 ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
		+	__TOC__
		+	</StructureSection>
	[[Category: Molodtsov, V]]		[[Category: Molodtsov, V]]
-	[[Category: Murakami, K.S]]	+	[[Category: Murakami, K S]]
		+	[[Category: Bacteriophage]]
		+	[[Category: N4]]
		+	[[Category: Rna polymerase]]
		+	[[Category: Transcription]]
		+	[[Category: Transcription-dna-rna complex]]

OCA: Protected "6dt8" [edit=sysop:move=sysop]

OCA — Wed, 27 Jun 2018 04:03:17 GMT

Protected "6dt8" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:03, 27 June 2018

OCA: New page: '''Unreleased structure''' The entry 6dt8 is ON HOLD Authors: Molodtsov, V., Murakami, K.S. Description: Bacteriophage N4 RNA polymerase II elongation complex 1 [[Category: Unreleased ...

OCA — Wed, 27 Jun 2018 04:03:16 GMT

New page: '''Unreleased structure''' The entry 6dt8 is ON HOLD Authors: Molodtsov, V., Murakami, K.S. Description: Bacteriophage N4 RNA polymerase II elongation complex 1 [[Category: Unreleased ...

New page

'''Unreleased structure'''

The entry 6dt8 is ON HOLD

Authors: Molodtsov, V., Murakami, K.S.

Description: Bacteriophage N4 RNA polymerase II elongation complex 1
[[Category: Unreleased Structures]]
[[Category: Molodtsov, V]]
[[Category: Murakami, K.S]]