6hms - Revision history

OCA at 01:27, 11 April 2020

OCA — Sat, 11 Apr 2020 01:27:00 GMT

←Older revision		Revision as of 01:27, 11 April 2020
Line 3:		Line 3:
	<SX load='6hms' size='340' side='right' viewer='molstar' caption='[[6hms]], [[Resolution\|resolution]] 7.10Å' scene=''>		<SX load='6hms' size='340' side='right' viewer='molstar' caption='[[6hms]], [[Resolution\|resolution]] 7.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6hms]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"pyrococcus_abyssi"_erauso_et_al._1993 "pyrococcus abyssi" erauso et al. 1993]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HMS OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6HMS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6hms]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"pyrococcus_abyssi"_erauso_et_al._1993 "pyrococcus abyssi" erauso et al. 1993]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HMS OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6HMS FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</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=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">polB, PYRAB01210, PAB2266 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=29292 "Pyrococcus abyssi" Erauso et al. 1993]), polC, PYRAB01200, PAB2404 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=29292 "Pyrococcus abyssi" Erauso et al. 1993])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">polB, PYRAB01210, PAB2266 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=29292 "Pyrococcus abyssi" Erauso et al. 1993]), polC, PYRAB01200, PAB2404 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=29292 "Pyrococcus abyssi" Erauso et al. 1993])</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=6hms FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6hms OCA], [http://pdbe.org/6hms PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6hms RCSB], [http://www.ebi.ac.uk/pdbsum/6hms PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6hms 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=6hms FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6hms OCA], [http://pdbe.org/6hms PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6hms RCSB], [http://www.ebi.ac.uk/pdbsum/6hms PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6hms ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 21:53, 6 March 2020

OCA — Fri, 06 Mar 2020 21:53:30 GMT

←Older revision		Revision as of 21:53, 6 March 2020
Line 1:		Line 1:

	==Cryo-EM map of DNA polymerase D from Pyrococcus abyssi in complex with DNA==		==Cryo-EM map of DNA polymerase D from Pyrococcus abyssi in complex with DNA==
-	<~~StructureSection~~ load='6hms' size='340' side='right'caption='[[6hms]], [[Resolution\|resolution]] 7.10Å' scene=''>	+	<SX load='6hms' size='340' side='right' viewer='molstar' caption='[[6hms]], [[Resolution\|resolution]] 7.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6hms]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"pyrococcus_abyssi"_erauso_et_al._1993 "pyrococcus abyssi" erauso et al. 1993]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HMS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6HMS FirstGlance]. <br>		<table><tr><td colspan='2'>[[6hms]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"pyrococcus_abyssi"_erauso_et_al._1993 "pyrococcus abyssi" erauso et al. 1993]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HMS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6HMS FirstGlance]. <br>
Line 25:		Line 25:
	<references/>		<references/>
	__TOC__		__TOC__
-	</~~StructureSection~~>	+	</SX>
	[[Category: Pyrococcus abyssi erauso et al. 1993]]		[[Category: Pyrococcus abyssi erauso et al. 1993]]
	[[Category: Large Structures]]		[[Category: Large Structures]]

OCA at 18:29, 11 December 2019

OCA — Wed, 11 Dec 2019 18:29:02 GMT

←Older revision		Revision as of 18:29, 11 December 2019
Line 1:		Line 1:

	==Cryo-EM map of DNA polymerase D from Pyrococcus abyssi in complex with DNA==		==Cryo-EM map of DNA polymerase D from Pyrococcus abyssi in complex with DNA==
-	<StructureSection load='6hms' size='340' side='right' caption='[[6hms]], [[Resolution\|resolution]] 7.10Å' scene=''>	+	<StructureSection load='6hms' size='340' side='right'caption='[[6hms]], [[Resolution\|resolution]] 7.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6hms]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HMS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6HMS FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6hms]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"pyrococcus_abyssi"_erauso_et_al._1993 "pyrococcus abyssi" erauso et al. 1993]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HMS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6HMS FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</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=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">polB, PYRAB01210, PAB2266 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=29292 "Pyrococcus abyssi" Erauso et al. 1993]), polC, PYRAB01200, PAB2404 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=29292 "Pyrococcus abyssi" Erauso et al. 1993])</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=6hms FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6hms OCA], [http://pdbe.org/6hms PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6hms RCSB], [http://www.ebi.ac.uk/pdbsum/6hms PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6hms ProSAT]</span></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=6hms FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6hms OCA], [http://pdbe.org/6hms PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6hms RCSB], [http://www.ebi.ac.uk/pdbsum/6hms PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6hms ProSAT]</span></td></tr>
	</table>		</table>
Line 18:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 6hms" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6hms" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[DNA polymerase 3D structures\|DNA polymerase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Pyrococcus abyssi erauso et al. 1993]]
		+	[[Category: Large Structures]]
	[[Category: Carroni, M]]		[[Category: Carroni, M]]
	[[Category: Raia, P]]		[[Category: Raia, P]]

OCA at 08:27, 30 January 2019

OCA — Wed, 30 Jan 2019 08:27:33 GMT

←Older revision		Revision as of 08:27, 30 January 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6hms is ~~ON HOLD~~	+	==Cryo-EM map of DNA polymerase D from Pyrococcus abyssi in complex with DNA==
		+	<StructureSection load='6hms' size='340' side='right' caption='[[6hms]], [[Resolution\|resolution]] 7.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6hms]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6HMS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6HMS FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6hms FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6hms OCA], [http://pdbe.org/6hms PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6hms RCSB], [http://www.ebi.ac.uk/pdbsum/6hms PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6hms ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DP2S_PYRAB DP2S_PYRAB]] Possesses two activities: a DNA synthesis (polymerase) and an exonucleolytic activity that degrades single-stranded DNA in the 3' to 5' direction. Has a template-primer preference which is characteristic of a replicative DNA polymerase (By similarity). [[http://www.uniprot.org/uniprot/DP2L_PYRAB DP2L_PYRAB]] Possesses two activities: a DNA synthesis (polymerase) and an exonucleolytic activity that degrades single-stranded DNA in the 3'- to 5'-direction. Has a template-primer preference which is characteristic of a replicative DNA polymerase (By similarity).
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	PolD is an archaeal replicative DNA polymerase (DNAP) made of a proofreading exonuclease subunit (DP1) and a larger polymerase catalytic subunit (DP2). Recently, we reported the individual crystal structures of the DP1 and DP2 catalytic cores, thereby revealing that PolD is an atypical DNAP that has all functional properties of a replicative DNAP but with the catalytic core of an RNA polymerase (RNAP). We now report the DNA-bound cryo-electron microscopy (cryo-EM) structure of the heterodimeric DP1-DP2 PolD complex from Pyrococcus abyssi, revealing a unique DNA-binding site. Comparison of PolD and RNAPs extends their structural similarities and brings to light the minimal catalytic core shared by all cellular transcriptases. Finally, elucidating the structure of the PolD DP1-DP2 interface, which is conserved in all eukaryotic replicative DNAPs, clarifies their evolutionary relationships with PolD and sheds light on the domain acquisition and exchange mechanism that occurred during the evolution of the eukaryotic replisome.

-	~~Authors~~:	+	Structure of the DP1-DP2 PolD complex bound with DNA and its implications for the evolutionary history of DNA and RNA polymerases.,Raia P, Carroni M, Henry E, Pehau-Arnaudet G, Brule S, Beguin P, Henneke G, Lindahl E, Delarue M, Sauguet L PLoS Biol. 2019 Jan 18;17(1):e3000122. doi: 10.1371/journal.pbio.3000122. PMID:30657780<ref>PMID:30657780</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 6hms" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Carroni, M]]
		+	[[Category: Raia, P]]
		+	[[Category: Sauguet, L]]
		+	[[Category: Dna]]
		+	[[Category: Polymerase d]]
		+	[[Category: Pyrococcus]]
		+	[[Category: Replication]]

OCA at 10:20, 16 January 2019

OCA — Wed, 16 Jan 2019 10:20:37 GMT

←Older revision		Revision as of 10:20, 16 January 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6hms is ON HOLD ~~until Paper Publication~~	+	The entry 6hms is ON HOLD

	Authors:		Authors:

OCA at 06:12, 17 October 2018

OCA — Wed, 17 Oct 2018 06:12:17 GMT

←Older revision		Revision as of 06:12, 17 October 2018
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors:		Authors:

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

OCA — Wed, 19 Sep 2018 18:14:48 GMT

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

←Older revision

Revision as of 18:14, 19 September 2018

OCA: New page: '''Unreleased structure''' The entry 6hms is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 19 Sep 2018 18:14:46 GMT

New page: '''Unreleased structure''' The entry 6hms is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6hms is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]