7n5j - Revision history

OCA at 16:24, 18 October 2023

OCA — Wed, 18 Oct 2023 16:24:31 GMT

←Older revision		Revision as of 16:24, 18 October 2023
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	<StructureSection load='7n5j' size='340' side='right'caption='[[7n5j]], [[Resolution\|resolution]] 2.82Å' scene=''>		<StructureSection load='7n5j' size='340' side='right'caption='[[7n5j]], [[Resolution\|resolution]] 2.82Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[7n5j]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7N5J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7N5J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7n5j]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermococcus_gammatolerans_EJ3 Thermococcus gammatolerans EJ3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7N5J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7N5J FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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]] 2.82Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=7n5j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7n5j OCA], [https://pdbe.org/7n5j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7n5j RCSB], [https://www.ebi.ac.uk/pdbsum/7n5j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7n5j 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=7n5j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7n5j OCA], [https://pdbe.org/7n5j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7n5j RCSB], [https://www.ebi.ac.uk/pdbsum/7n5j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7n5j ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/PCNA_THEGJ PCNA_THEGJ]] Sliding clamp subunit that acts as a moving platform for DNA processing. Responsible for tethering the catalytic subunit of DNA polymerase and other proteins to DNA during high-speed replication.	+	[https://www.uniprot.org/uniprot/PCNA_THEGJ PCNA_THEGJ] Sliding clamp subunit that acts as a moving platform for DNA processing. Responsible for tethering the catalytic subunit of DNA polymerase and other proteins to DNA during high-speed replication.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 7n5j" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 7n5j" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Proliferating cell nuclear antigen 3D structures\|Proliferating cell nuclear antigen 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Marin-Tovar, Y]]	+	[[Category: Thermococcus gammatolerans EJ3]]
-	[[Category: Rudino-Pinera, E]]	+	[[Category: Marin-Tovar Y]]
-	~~[[Category: Dna binding protein]]~~	+	[[Category: Rudino-Pinera E]]
-	~~[[Category: Ionizing radiation]]~~	+
-	~~[[Category: Pcna]]~~	+
-	~~[[Category: Radiation damage]]~~	+
-	~~[[Category: Radioresistance]]~~	+
-	~~[[Category: Sliding clamp~~]]	+

OCA at 06:35, 18 August 2022

OCA — Thu, 18 Aug 2022 06:35:15 GMT

←Older revision		Revision as of 06:35, 18 August 2022
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	==PCNA from Thermococcus gammatolerans: crystal I, collection 5, 2.82 A, 89.1 MGy==		==PCNA from Thermococcus gammatolerans: crystal I, collection 5, 2.82 A, 89.1 MGy==
-	<StructureSection load='7n5j' size='340' side='right'caption='[[7n5j]]' scene=''>	+	<StructureSection load='7n5j' size='340' side='right'caption='[[7n5j]], [[Resolution\|resolution]] 2.82Å' 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=7N5J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7N5J FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[7n5j]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7N5J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7N5J 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=7n5j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7n5j OCA], [https://pdbe.org/7n5j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7n5j RCSB], [https://www.ebi.ac.uk/pdbsum/7n5j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7n5j ProSAT]</span></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=7n5j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7n5j OCA], [https://pdbe.org/7n5j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7n5j RCSB], [https://www.ebi.ac.uk/pdbsum/7n5j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7n5j ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[https://www.uniprot.org/uniprot/PCNA_THEGJ PCNA_THEGJ]] Sliding clamp subunit that acts as a moving platform for DNA processing. Responsible for tethering the catalytic subunit of DNA polymerase and other proteins to DNA during high-speed replication.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Proliferating cell nuclear antigen (PCNA) is an essential protein for cell viability in archaea and eukarya, since it is involved in DNA replication and repair. In order to obtain insights regarding the characteristics that confer radioresistance, the structural study of the PCNA from Thermococcus gammatolerans (PCNATg ) in a gradient of ionizing radiation by X-ray crystallography was carried out, together with a bioinformatic analysis of homotrimeric PCNA structures, their sequences, and their molecular interactions. The results obtained from the datasets and the accumulated radiation dose for the last collection from three crystals revealed moderate and localized damage, since even with the loss of resolution, the electron density map corresponding to the last collection allowed to build the whole structure. Attempting to understand this behavior, multiple sequence alignments, and structural superpositions were performed, revealing that PCNA is a protein with a poorly conserved sequence, but with a highly conserved structure. The PCNATg presented the highest percentage of charged residues, mostly negatively charged, with a proportion of glutamate more than double aspartate, lack of cysteines and tryptophan, besides a high number of salt bridges. The structural study by X-ray crystallography reveals that the PCNATg has the intrinsic ability to resist high levels of ionizing radiation, and the bioinformatic analysis suggests that molecular evolution selected a particular composition of amino acid residues, and their consequent network of synergistic interactions for extreme conditions, as a collateral effect, conferring radioresistance to a protein involved in the chromosomal DNA metabolism of a radioresistant microorganism.
		+
		+	PCNA from Thermococcus gammatolerans: A protein involved in chromosomal DNA metabolism intrinsically resistant at high levels of ionizing radiation.,Marin-Tovar Y, Serrano-Posada H, Diaz-Vilchis A, Rudino-Pinera E Proteins. 2022 Apr 18. doi: 10.1002/prot.26346. PMID:35435259<ref>PMID:35435259</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 7n5j" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Marin-Tovar Y]]	+	[[Category: Marin-Tovar, Y]]
-	[[Category: Rudino-Pinera E]]	+	[[Category: Rudino-Pinera, E]]
		+	[[Category: Dna binding protein]]
		+	[[Category: Ionizing radiation]]
		+	[[Category: Pcna]]
		+	[[Category: Radiation damage]]
		+	[[Category: Radioresistance]]
		+	[[Category: Sliding clamp]]

OCA at 12:47, 4 May 2022

OCA — Wed, 04 May 2022 12:47:12 GMT

←Older revision		Revision as of 12:47, 4 May 2022
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-	'''Unreleased structure'''

-	~~The entry 7n5j is ON HOLD until Paper Publication~~	+	==PCNA from Thermococcus gammatolerans: crystal I, collection 5, 2.82 A, 89.1 MGy==
-		+	<StructureSection load='7n5j' size='340' side='right'caption='[[7n5j]]' scene=''>
-	~~Authors: Marin-Tovar, Y., Rudino-Pinera, E.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7N5J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7N5J FirstGlance]. <br>
-	~~Description:~~ PCNA from Thermococcus gammatolerans: crystal I, collection 5, 2.82 A, 89.1 MGy	+	</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=7n5j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7n5j OCA], [https://pdbe.org/7n5j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7n5j RCSB], [https://www.ebi.ac.uk/pdbsum/7n5j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7n5j ProSAT]</span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	</table>
-	[[Category: Marin-Tovar, Y]]	+	__TOC__
-	[[Category: Rudino-Pinera, E]]	+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Marin-Tovar Y]]
		+	[[Category: Rudino-Pinera E]]

OCA at 08:46, 14 July 2021

OCA — Wed, 14 Jul 2021 08:46:19 GMT

←Older revision		Revision as of 08:46, 14 July 2021
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 7n5j is ON HOLD	+	The entry 7n5j is ON HOLD until Paper Publication

	Authors: Marin-Tovar, Y., Rudino-Pinera, E.		Authors: Marin-Tovar, Y., Rudino-Pinera, E.

OCA: Protected "7n5j" [edit=sysop:move=sysop]

OCA — Thu, 17 Jun 2021 13:39:40 GMT

Protected "7n5j" [edit=sysop:move=sysop]

←Older revision

Revision as of 13:39, 17 June 2021

OCA: New page: '''Unreleased structure''' The entry 7n5j is ON HOLD Authors: Marin-Tovar, Y., Rudino-Pinera, E. Description: PCNA from Thermococcus gammatolerans: crystal I, collection 5, 2.82 A, 89....

OCA — Thu, 17 Jun 2021 13:39:39 GMT

New page: '''Unreleased structure''' The entry 7n5j is ON HOLD Authors: Marin-Tovar, Y., Rudino-Pinera, E. Description: PCNA from Thermococcus gammatolerans: crystal I, collection 5, 2.82 A, 89....

New page

'''Unreleased structure'''

The entry 7n5j is ON HOLD

Authors: Marin-Tovar, Y., Rudino-Pinera, E.

Description: PCNA from Thermococcus gammatolerans: crystal I, collection 5, 2.82 A, 89.1 MGy
[[Category: Unreleased Structures]]
[[Category: Marin-Tovar, Y]]
[[Category: Rudino-Pinera, E]]