5v7m - Revision history

OCA at 14:31, 6 March 2024

OCA — Wed, 06 Mar 2024 14:31:26 GMT

←Older revision		Revision as of 14:31, 6 March 2024
Line 3:		Line 3:
	<StructureSection load='5v7m' size='340' side='right'caption='[[5v7m]], [[Resolution\|resolution]] 1.93Å' scene=''>		<StructureSection load='5v7m' size='340' side='right'caption='[[5v7m]], [[Resolution\|resolution]] 1.93Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5v7m]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Baker's_yeast Baker's yeast~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V7M OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5V7M FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5v7m]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V7M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5V7M 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~~></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]] 1.93Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~POL30, YBR088C, YBR0811 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=559292 Baker~~'~~s yeast])~~</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></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=5v7m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v7m OCA], [~~http~~://pdbe.org/5v7m PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5v7m RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5v7m PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5v7m 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=5v7m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v7m OCA], [https://pdbe.org/5v7m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5v7m RCSB], [https://www.ebi.ac.uk/pdbsum/5v7m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5v7m ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/PCNA_YEAST PCNA_YEAST]] This protein is an auxiliary protein of DNA polymerase delta and is involved in the control of eukaryotic DNA replication by increasing the polymerase's processibility during elongation of the leading strand. Involved in DNA repair.<ref>PMID:11545742</ref> <ref>PMID:12226657</ref>	+	[https://www.uniprot.org/uniprot/PCNA_YEAST PCNA_YEAST] This protein is an auxiliary protein of DNA polymerase delta and is involved in the control of eukaryotic DNA replication by increasing the polymerase's processibility during elongation of the leading strand. Involved in DNA repair.<ref>PMID:11545742</ref> <ref>PMID:12226657</ref>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Proliferating cell nuclear antigen (PCNA), a homotrimeric protein, is the eukaryotic sliding clamp that functions as a processivity factor for polymerases during DNA replication. Chromatin association factor 1 (CAF-1) is a heterotrimeric histone chaperone protein that is required for coupling chromatin assembly with DNA replication in eukaryotes. CAF-1 association with replicating DNA, and the targeting of newly synthesized histones to sites of DNA replication and repair requires its interaction with PCNA. Genetic studies have identified three mutant forms of PCNA in yeast that cause defects in gene silencing and exhibit altered association of CAF-1 to chromatin in vivo, as well as inhibit binding to CAF-1 in vitro. Three of these mutant forms of PCNA, encoded by the pol30-6, pol30-8, and the pol30-79 alleles, direct the synthesis of PCNA proteins with the amino acid substitutions D41A/D42A, R61A/D63A, and L126A/I128A, respectively. Interestingly, these double alanine substitutions are located far away from each other within the PCNA protein. To understand the structural basis of the interaction between PCNA and CAF-1 and how disruption of this interaction leads to reduced gene silencing, we determined the X-ray crystal structures of each of these mutant PCNA proteins. All three of the substitutions caused disruptions of a surface cavity on the front face of the PCNA ring, which is formed in part by three loops comprised of residues 21-24, 41-44, and 118-134. We suggest that this cavity is a novel binding pocket required for the interaction between PCNA and CAF-1, and that this region in PCNA also represents a potential binding site for other PCNA-binding proteins.	+
-		+
-	Crystal structures of PCNA mutant proteins defective in gene silencing suggest a novel interaction site on the front face of the PCNA ring.,Kondratick CM, Litman JM, Shaffer KV, Washington MT, Dieckman LM PLoS One. 2018 Mar 2;13(3):e0193333. doi: 10.1371/journal.pone.0193333., eCollection 2018. PMID:29499038<ref>PMID:29499038</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 5v7m" style="background-color:#fffaf0;"></div~~>	+

	==See Also==		==See Also==
Line 26:		Line 17:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Baker's yeast]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Dieckman, L M~~]]	+	[[Category: Saccharomyces cerevisiae S288C]]
-	[[Category: ~~Kondratick, C M~~]]	+	[[Category: Dieckman LM]]
-	[[Category: ~~Litman, J M~~]]	+	[[Category: Kondratick CM]]
-	[[Category: ~~Washington, M T~~]]	+	[[Category: Litman JM]]
-	[[Category: ~~Caf-1]]~~	+	[[Category: Washington MT]]
-	~~[[Category: Dna binding protein~~]]	+

OCA at 09:29, 1 January 2020

OCA — Wed, 01 Jan 2020 09:29:41 GMT

←Older revision		Revision as of 09:29, 1 January 2020
Line 1:		Line 1:

	==PCNA mutant L126A/I128A Protein Defective in Gene Silencing==		==PCNA mutant L126A/I128A Protein Defective in Gene Silencing==
-	<StructureSection load='5v7m' size='340' side='right' caption='[[5v7m]], [[Resolution\|resolution]] 1.93Å' scene=''>	+	<StructureSection load='5v7m' size='340' side='right'caption='[[5v7m]], [[Resolution\|resolution]] 1.93Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5v7m]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V7M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5V7M FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5v7m]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V7M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5V7M 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></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></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">POL30, YBR088C, YBR0811 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</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=5v7m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v7m OCA], [http://pdbe.org/5v7m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5v7m RCSB], [http://www.ebi.ac.uk/pdbsum/5v7m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5v7m 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=5v7m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v7m OCA], [http://pdbe.org/5v7m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5v7m RCSB], [http://www.ebi.ac.uk/pdbsum/5v7m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5v7m ProSAT]</span></td></tr>
	</table>		</table>
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	</div>		</div>
	<div class="pdbe-citations 5v7m" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5v7m" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Proliferating cell nuclear antigen 3D structures\|Proliferating cell nuclear antigen 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Baker's yeast]]
		+	[[Category: Large Structures]]
	[[Category: Dieckman, L M]]		[[Category: Dieckman, L M]]
	[[Category: Kondratick, C M]]		[[Category: Kondratick, C M]]

OCA at 06:23, 14 March 2018

OCA — Wed, 14 Mar 2018 06:23:49 GMT

←Older revision		Revision as of 06:23, 14 March 2018
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5v7m is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==PCNA mutant L126A/I128A Protein Defective in Gene Silencing==
		+	<StructureSection load='5v7m' size='340' side='right' caption='[[5v7m]], [[Resolution\|resolution]] 1.93Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5v7m]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V7M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5V7M 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></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=5v7m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v7m OCA], [http://pdbe.org/5v7m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5v7m RCSB], [http://www.ebi.ac.uk/pdbsum/5v7m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5v7m ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PCNA_YEAST PCNA_YEAST]] This protein is an auxiliary protein of DNA polymerase delta and is involved in the control of eukaryotic DNA replication by increasing the polymerase's processibility during elongation of the leading strand. Involved in DNA repair.<ref>PMID:11545742</ref> <ref>PMID:12226657</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Proliferating cell nuclear antigen (PCNA), a homotrimeric protein, is the eukaryotic sliding clamp that functions as a processivity factor for polymerases during DNA replication. Chromatin association factor 1 (CAF-1) is a heterotrimeric histone chaperone protein that is required for coupling chromatin assembly with DNA replication in eukaryotes. CAF-1 association with replicating DNA, and the targeting of newly synthesized histones to sites of DNA replication and repair requires its interaction with PCNA. Genetic studies have identified three mutant forms of PCNA in yeast that cause defects in gene silencing and exhibit altered association of CAF-1 to chromatin in vivo, as well as inhibit binding to CAF-1 in vitro. Three of these mutant forms of PCNA, encoded by the pol30-6, pol30-8, and the pol30-79 alleles, direct the synthesis of PCNA proteins with the amino acid substitutions D41A/D42A, R61A/D63A, and L126A/I128A, respectively. Interestingly, these double alanine substitutions are located far away from each other within the PCNA protein. To understand the structural basis of the interaction between PCNA and CAF-1 and how disruption of this interaction leads to reduced gene silencing, we determined the X-ray crystal structures of each of these mutant PCNA proteins. All three of the substitutions caused disruptions of a surface cavity on the front face of the PCNA ring, which is formed in part by three loops comprised of residues 21-24, 41-44, and 118-134. We suggest that this cavity is a novel binding pocket required for the interaction between PCNA and CAF-1, and that this region in PCNA also represents a potential binding site for other PCNA-binding proteins.

-	~~Authors: Kondratick, C.M~~., Litman, ~~J.M.~~, Washington, M.T.~~, Dieckman, L~~.M.	+	Crystal structures of PCNA mutant proteins defective in gene silencing suggest a novel interaction site on the front face of the PCNA ring.,Kondratick CM, Litman JM, Shaffer KV, Washington MT, Dieckman LM PLoS One. 2018 Mar 2;13(3):e0193333. doi: 10.1371/journal.pone.0193333., eCollection 2018. PMID:29499038<ref>PMID:29499038</ref>

-	~~Description~~: ~~PCNA mutant L126A~~/~~I128A Protein Defective in Gene Silencing~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: Litman, J.M]]	+	<div class="pdbe-citations 5v7m" style="background-color:#fffaf0;"></div>
-	[[Category: Washington, M.T]]	+	== References ==
-	[[Category: ~~Kondratick, C.M~~]]	+	<references/>
-	[[Category: ~~Dieckman, L.M~~]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Dieckman, L M]]
		+	[[Category: Kondratick, C M]]
		+	[[Category: Litman, J M]]
		+	[[Category: Washington, M T]]
		+	[[Category: Caf-1]]
		+	[[Category: Dna binding protein]]

OCA at 13:55, 27 September 2017

OCA — Wed, 27 Sep 2017 13:55:42 GMT

←Older revision		Revision as of 13:55, 27 September 2017
Line 8:		Line 8:
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Litman, J.M]]		[[Category: Litman, J.M]]
		+	[[Category: Washington, M.T]]
	[[Category: Kondratick, C.M]]		[[Category: Kondratick, C.M]]
	[[Category: Dieckman, L.M]]		[[Category: Dieckman, L.M]]
-	[[Category: Washington, M.T]]

OCA at 09:42, 12 April 2017

OCA — Wed, 12 Apr 2017 09:42:21 GMT

←Older revision		Revision as of 09:42, 12 April 2017
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5v7m is ON HOLD	+	The entry 5v7m is ON HOLD until Paper Publication

	Authors: Kondratick, C.M., Litman, J.M., Washington, M.T., Dieckman, L.M.		Authors: Kondratick, C.M., Litman, J.M., Washington, M.T., Dieckman, L.M.

OCA: Protected "5v7m" [edit=sysop:move=sysop]

OCA — Wed, 05 Apr 2017 11:41:56 GMT

Protected "5v7m" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:41, 5 April 2017

OCA: New page: '''Unreleased structure''' The entry 5v7m is ON HOLD Authors: Kondratick, C.M., Litman, J.M., Washington, M.T., Dieckman, L.M. Description: PCNA mutant L126A/I128A Protein Defective in...

OCA — Wed, 05 Apr 2017 11:41:55 GMT

New page: '''Unreleased structure''' The entry 5v7m is ON HOLD Authors: Kondratick, C.M., Litman, J.M., Washington, M.T., Dieckman, L.M. Description: PCNA mutant L126A/I128A Protein Defective in...

New page

'''Unreleased structure'''

The entry 5v7m is ON HOLD

Authors: Kondratick, C.M., Litman, J.M., Washington, M.T., Dieckman, L.M.

Description: PCNA mutant L126A/I128A Protein Defective in Gene Silencing
[[Category: Unreleased Structures]]
[[Category: Litman, J.M]]
[[Category: Kondratick, C.M]]
[[Category: Dieckman, L.M]]
[[Category: Washington, M.T]]