6n9x - Revision history

OCA at 03:14, 11 April 2020

2020-04-11T03:14:50Z

←Older revision		Revision as of 03:14, 11 April 2020
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	<SX load='6n9x' size='340' side='right' viewer='molstar' caption='[[6n9x]], [[Resolution\|resolution]] 4.10Å' scene=''>		<SX load='6n9x' size='340' side='right' viewer='molstar' caption='[[6n9x]], [[Resolution\|resolution]] 4.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6n9x]] is a 9 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpt7 Bpt7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N9X OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6N9X FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6n9x]] is a 9 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpt7 Bpt7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N9X OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6N9X FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TTP:THYMIDINE-5-TRIPHOSPHATE'>TTP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>	+	</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=TTP:THYMIDINE-5-TRIPHOSPHATE'>TTP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6n7i\|6n7i]], [[6n7n\|6n7n]], [[6n7s\|6n7s]], [[6n7t\|6n7t]], [[6n7v\|6n7v]], [[6n7w\|6n7w]], [[6n9u\|6n9u]], [[6n9v\|6n9v]], [[6n9w\|6n9w]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6n7i\|6n7i]], [[6n7n\|6n7n]], [[6n7s\|6n7s]], [[6n7t\|6n7t]], [[6n7v\|6n7v]], [[6n7w\|6n7w]], [[6n9u\|6n9u]], [[6n9v\|6n9v]], [[6n9w\|6n9w]]</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=6n9x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n9x OCA], [http://pdbe.org/6n9x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6n9x RCSB], [http://www.ebi.ac.uk/pdbsum/6n9x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6n9x ProSAT]</span></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=6n9x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n9x OCA], [http://pdbe.org/6n9x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6n9x RCSB], [http://www.ebi.ac.uk/pdbsum/6n9x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6n9x ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 22:48, 6 March 2020

2020-03-06T22:48:11Z

←Older revision		Revision as of 22:48, 6 March 2020
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	==Structure of bacteriophage T7 lagging-strand DNA polymerase (D5A/E7A) and gp4 (helicase/primase) bound to DNA including RNA/DNA hybrid, and an incoming dTTP (LagS3)==		==Structure of bacteriophage T7 lagging-strand DNA polymerase (D5A/E7A) and gp4 (helicase/primase) bound to DNA including RNA/DNA hybrid, and an incoming dTTP (LagS3)==
-	<~~StructureSection~~ load='6n9x' size='340' side='right'caption='[[6n9x]], [[Resolution\|resolution]] 4.10Å' scene=''>	+	<SX load='6n9x' size='340' side='right' viewer='molstar' caption='[[6n9x]], [[Resolution\|resolution]] 4.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6n9x]] is a 9 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpt7 Bpt7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N9X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6N9X FirstGlance]. <br>		<table><tr><td colspan='2'>[[6n9x]] is a 9 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpt7 Bpt7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N9X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6N9X FirstGlance]. <br>
Line 23:		Line 23:
	==See Also==		==See Also==
	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]		*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
		+	*[[RNA polymerase 3D structures\|RNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
-	</~~StructureSection~~>	+	</SX>
	[[Category: Bpt7]]		[[Category: Bpt7]]
	[[Category: Large Structures]]		[[Category: Large Structures]]

OCA at 11:23, 18 December 2019

2019-12-18T11:23:48Z

←Older revision		Revision as of 11:23, 18 December 2019
Line 1:		Line 1:

	==Structure of bacteriophage T7 lagging-strand DNA polymerase (D5A/E7A) and gp4 (helicase/primase) bound to DNA including RNA/DNA hybrid, and an incoming dTTP (LagS3)==		==Structure of bacteriophage T7 lagging-strand DNA polymerase (D5A/E7A) and gp4 (helicase/primase) bound to DNA including RNA/DNA hybrid, and an incoming dTTP (LagS3)==
-	<StructureSection load='6n9x' size='340' side='right' caption='[[6n9x]], [[Resolution\|resolution]] 4.10Å' scene=''>	+	<StructureSection load='6n9x' size='340' side='right'caption='[[6n9x]], [[Resolution\|resolution]] 4.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6n9x]] is a 9 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N9X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6N9X FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6n9x]] is a 9 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpt7 Bpt7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N9X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6N9X FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TTP:THYMIDINE-5-TRIPHOSPHATE'>TTP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TTP:THYMIDINE-5-TRIPHOSPHATE'>TTP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene></td></tr>
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	</div>		</div>
	<div class="pdbe-citations 6n9x" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6n9x" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bpt7]]
		+	[[Category: Large Structures]]
	[[Category: Fox, T]]		[[Category: Fox, T]]
	[[Category: Gao, Y]]		[[Category: Gao, Y]]

OCA at 07:35, 6 March 2019

2019-03-06T07:35:13Z

←Older revision		Revision as of 07:35, 6 March 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6n9x is ~~ON HOLD~~	+	==Structure of bacteriophage T7 lagging-strand DNA polymerase (D5A/E7A) and gp4 (helicase/primase) bound to DNA including RNA/DNA hybrid, and an incoming dTTP (LagS3)==
		+	<StructureSection load='6n9x' size='340' side='right' caption='[[6n9x]], [[Resolution\|resolution]] 4.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6n9x]] is a 9 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6N9X OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6N9X FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TTP:THYMIDINE-5-TRIPHOSPHATE'>TTP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DOC:2,3-DIDEOXYCYTIDINE-5-MONOPHOSPHATE'>DOC</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6n7i\|6n7i]], [[6n7n\|6n7n]], [[6n7s\|6n7s]], [[6n7t\|6n7t]], [[6n7v\|6n7v]], [[6n7w\|6n7w]], [[6n9u\|6n9u]], [[6n9v\|6n9v]], [[6n9w\|6n9w]]</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=6n9x FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6n9x OCA], [http://pdbe.org/6n9x PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6n9x RCSB], [http://www.ebi.ac.uk/pdbsum/6n9x PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6n9x ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PRIM_BPT7 PRIM_BPT7]] Synthesizes short RNA primers for DNA replication. Unwinds the DNA at the replication forks and generates single-stranded DNA for both leading and lagging strand synthesis. The primase synthesizes short RNA primers on the lagging strand that the polymerase elongates using dNTPs.<ref>PMID:9096333</ref> <ref>PMID:21606333</ref> <ref>PMID:22977246</ref> [[http://www.uniprot.org/uniprot/DPOL_BPT7 DPOL_BPT7]] Replicates viral genomic DNA. Non-processive DNA polymerase that achieves processivity by binding to host thioredoxin (TrxA). This interaction increases the rate of dNTP incorporation to yield a processivity of approximately 800 nucleotides (nt) per binding event. Interacts with DNA helicase gp4 to coordinate nucleotide polymerization with unwinding of the DNA. The leading strand is synthesized continuously while synthesis of the lagging strand requires the synthesis of oligoribonucleotides by the primase domain of gp4.<ref>PMID:9218486</ref> <ref>PMID:21606333</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Visualization in atomic detail of the replisome that performs concerted leading- and lagging-DNA strand synthesis at a replication fork has not been reported. Using bacteriophage T7 as a model system, we determined cryo-electron microscopy structures up to 3.2-angstroms resolution of helicase translocating along DNA and of helicase-polymerase-primase complexes engaging in synthesis of both DNA strands. Each domain of the spiral-shaped hexameric helicase translocates sequentially hand-over-hand along a single-stranded DNA coil, akin to the way AAA+ ATPases (adenosine triphosphatases) unfold peptides. Two lagging-strand polymerases are attached to the primase, ready for Okazaki fragment synthesis in tandem. A beta hairpin from the leading-strand polymerase separates two parental DNA strands into a T-shaped fork, thus enabling the closely coupled helicase to advance perpendicular to the downstream DNA duplex. These structures reveal the molecular organization and operating principles of a replisome.

-	~~Authors:~~ Gao, Y., Fox, T., ~~Val~~, N., ~~Yang~~, W.	+	Structures and operating principles of the replisome.,Gao Y, Cui Y, Fox T, Lin S, Wang H, de Val N, Zhou ZH, Yang W Science. 2019 Feb 22;363(6429). pii: science.aav7003. doi:, 10.1126/science.aav7003. Epub 2019 Jan 24. PMID:30679383<ref>PMID:30679383</ref>

-	~~Description: Structure~~ of ~~gp5 DNA polymerase binding to B and C subunits~~ of ~~gp4 primase~~-~~helicase hexamer complexed with trx, RNA~~/~~DNA hybrid, and incoming dTTP (LagS3)~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 6n9x" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Fox, T]]
	[[Category: Gao, Y]]		[[Category: Gao, Y]]
	[[Category: Val, N]]		[[Category: Val, N]]
-	[[Category: Fox, T]]
	[[Category: Yang, W]]		[[Category: Yang, W]]
		+	[[Category: Dna polymerase]]
		+	[[Category: Dna replication]]
		+	[[Category: Helicase]]
		+	[[Category: Hydrolase]]
		+	[[Category: Primase]]
		+	[[Category: Replisome]]
		+	[[Category: Transferase-dna complex]]

OCA: Protected "6n9x" [edit=sysop:move=sysop]

2018-12-12T05:23:52Z

Protected "6n9x" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:23, 12 December 2018

OCA: New page: '''Unreleased structure''' The entry 6n9x is ON HOLD Authors: Gao, Y., Fox, T., Val, N., Yang, W. Description: Structure of gp5 DNA polymerase binding to B and C subunits of gp4 primas...

2018-12-12T05:23:51Z

New page: '''Unreleased structure''' The entry 6n9x is ON HOLD Authors: Gao, Y., Fox, T., Val, N., Yang, W. Description: Structure of gp5 DNA polymerase binding to B and C subunits of gp4 primas...

New page

'''Unreleased structure'''

The entry 6n9x is ON HOLD

Authors: Gao, Y., Fox, T., Val, N., Yang, W.

Description: Structure of gp5 DNA polymerase binding to B and C subunits of gp4 primase-helicase hexamer complexed with trx, RNA/DNA hybrid, and incoming dTTP (LagS3)
[[Category: Unreleased Structures]]
[[Category: Gao, Y]]
[[Category: Val, N]]
[[Category: Fox, T]]
[[Category: Yang, W]]