6cqo - Revision history

OCA at 10:16, 26 February 2020

OCA — Wed, 26 Feb 2020 10:16:59 GMT

←Older revision		Revision as of 10:16, 26 February 2020
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	==See Also==		==See Also==
-	*[[Single-stranded DNA-binding protein\|Single-stranded DNA-binding protein]]	+	*[[Single-stranded DNA-binding protein 3D structures\|Single-stranded DNA-binding protein 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 10:49, 1 January 2020

OCA — Wed, 01 Jan 2020 10:49:41 GMT

←Older revision		Revision as of 10:49, 1 January 2020
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	==Crystal Structure of mitochondrial single-stranded DNA binding proteins from S. cerevisiae (SeMet Labeled), Rim1 (Form2)==		==Crystal Structure of mitochondrial single-stranded DNA binding proteins from S. cerevisiae (SeMet Labeled), Rim1 (Form2)==
-	<StructureSection load='6cqo' size='340' side='right' caption='[[6cqo]], [[Resolution\|resolution]] 2.80Å' scene=''>	+	<StructureSection load='6cqo' size='340' side='right'caption='[[6cqo]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6cqo]] is a 8 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=6CQO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CQO FirstGlance]. <br>		<table><tr><td colspan='2'>[[6cqo]] is a 8 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=6CQO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CQO FirstGlance]. <br>
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	</StructureSection>		</StructureSection>
	[[Category: Baker's yeast]]		[[Category: Baker's yeast]]
		+	[[Category: Large Structures]]
	[[Category: Bona, P D]]		[[Category: Bona, P D]]
	[[Category: Edwin, A]]		[[Category: Edwin, A]]

OCA at 06:30, 18 October 2018

OCA — Thu, 18 Oct 2018 06:30:30 GMT

←Older revision		Revision as of 06:30, 18 October 2018
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	</div>		</div>
	<div class="pdbe-citations 6cqo" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6cqo" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Single-stranded DNA-binding protein\|Single-stranded DNA-binding protein]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:41, 4 July 2018

OCA — Wed, 04 Jul 2018 07:41:34 GMT

←Older revision		Revision as of 07:41, 4 July 2018
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	<StructureSection load='6cqo' size='340' side='right' caption='[[6cqo]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='6cqo' size='340' side='right' caption='[[6cqo]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6cqo]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CQO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CQO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6cqo]] is a 8 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=6CQO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CQO FirstGlance]. <br>
	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RIM1, YCR028C-A, YCR28C-A ([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=6cqo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cqo OCA], [http://pdbe.org/6cqo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6cqo RCSB], [http://www.ebi.ac.uk/pdbsum/6cqo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6cqo 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=6cqo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cqo OCA], [http://pdbe.org/6cqo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6cqo RCSB], [http://www.ebi.ac.uk/pdbsum/6cqo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6cqo ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/RIM1_YEAST RIM1_YEAST]] This protein binds preferentially and cooperatively to single-stranded DNA (ssDNS). Involved in mitochondrial DNA replication. Stimulates PIF1 helicase activity.<ref>PMID:23175612</ref>		[[http://www.uniprot.org/uniprot/RIM1_YEAST RIM1_YEAST]] This protein binds preferentially and cooperatively to single-stranded DNA (ssDNS). Involved in mitochondrial DNA replication. Stimulates PIF1 helicase activity.<ref>PMID:23175612</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Rim1 is the mitochondrial single-stranded DNA binding protein in Saccharomyces cerevisiae and functions to coordinate replication and maintenance of mtDNA. Rim1 can form homo-tetramers in solution and this species has been assumed to be solely responsible for ssDNA binding. We solved structures of tetrameric Rim1 in two crystals forms which differ in the relative orientation of the dimers within the tetramer. In testing whether the different arrangement of the dimers was due to formation of unstable tetramers, we discovered that while Rim1 forms tetramers at high protein concentration, it dissociates into a smaller oligomeric species at low protein concentrations. A single point mutation at the dimer-dimer interface generates stable dimers and provides support for a dimer-tetramer oligomerization model. The presence of Rim1 dimers in solution becomes evident in DNA binding studies using short ssDNA substrates. However, binding of the first Rim1 dimer is followed by binding of a second dimer, whose affinity depends on the length of the ssDNA. We propose a model where binding of DNA to a dimer of Rim1 induces tetramerization, modulated by the ability of the second dimer to interact with ssDNA.
		+
		+	The mitochondrial single-stranded DNA binding protein from S. cerevisiae, Rim1, does not form stable homo-tetramers and binds DNA as a dimer of dimers.,Singh SP, Kukshal V, De Bona P, Antony E, Galletto R Nucleic Acids Res. 2018 Jun 21. pii: 5042044. doi: 10.1093/nar/gky530. PMID:29931186<ref>PMID:29931186</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6cqo" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Baker's yeast]]
	[[Category: Bona, P D]]		[[Category: Bona, P D]]
	[[Category: Edwin, A]]		[[Category: Edwin, A]]

OCA at 05:35, 30 May 2018

OCA — Wed, 30 May 2018 05:35:24 GMT

←Older revision		Revision as of 05:35, 30 May 2018
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-	'''Unreleased structure'''

-	~~The entry 6cqo is ON HOLD until Paper Publication~~	+	==Crystal Structure of mitochondrial single-stranded DNA binding proteins from S. cerevisiae (SeMet Labeled), Rim1 (Form2)==
-		+	<StructureSection load='6cqo' size='340' side='right' caption='[[6cqo]], [[Resolution\|resolution]] 2.80Å' scene=''>
-	~~Authors: Singh, S.P., Kukshal, V., Bona, P.D., Lytle, A.K., Edwin, A., Galletto, R.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6cqo]] is a 8 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CQO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CQO FirstGlance]. <br>
-	~~Description:~~ Crystal Structure of mitochondrial single-stranded DNA binding proteins from S. cerevisiae (SeMet Labeled), Rim1 (Form2)	+	</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	<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=6cqo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cqo OCA], [http://pdbe.org/6cqo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6cqo RCSB], [http://www.ebi.ac.uk/pdbsum/6cqo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6cqo ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Kukshal, V~~]]	+	</table>
-	[[~~Category~~: ~~Lytle~~, A.K]]	+	== Function ==
-	[[~~Category~~: ~~Bona, P~~.D]]	+	[[http://www.uniprot.org/uniprot/RIM1_YEAST RIM1_YEAST]] This protein binds preferentially and cooperatively to single-stranded DNA (ssDNS). Involved in mitochondrial DNA replication. Stimulates PIF1 helicase activity.<ref>PMID:23175612</ref>
-	[[Category: ~~Singh~~, S.P]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Bona, P D]]
	[[Category: Edwin, A]]		[[Category: Edwin, A]]
	[[Category: Galletto, R]]		[[Category: Galletto, R]]
		+	[[Category: Kukshal, V]]
		+	[[Category: Lytle, A K]]
		+	[[Category: Singh, S P]]
		+	[[Category: Dna binding protein]]
		+	[[Category: Mitochondrial single-stranded dna binding protein]]
		+	[[Category: Rim1]]
		+	[[Category: S. cerevisiae]]

OCA at 12:26, 11 April 2018

OCA — Wed, 11 Apr 2018 12:26:00 GMT

←Older revision		Revision as of 12:26, 11 April 2018
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	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Singh, S.P., Kukshal, V., Bona, P.D., Lytle, A.K., Edwin, A., Galletto, R.		Authors: Singh, S.P., Kukshal, V., Bona, P.D., Lytle, A.K., Edwin, A., Galletto, R.

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

OCA — Wed, 21 Mar 2018 06:15:35 GMT

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

←Older revision

Revision as of 06:15, 21 March 2018

OCA: New page: '''Unreleased structure''' The entry 6cqo is ON HOLD Authors: Singh, S.P., Kukshal, V., Bona, P.D., Lytle, A.K., Edwin, A., Galletto, R. Description: Crystal Structure of mitochondrial...

OCA — Wed, 21 Mar 2018 06:15:34 GMT

New page: '''Unreleased structure''' The entry 6cqo is ON HOLD Authors: Singh, S.P., Kukshal, V., Bona, P.D., Lytle, A.K., Edwin, A., Galletto, R. Description: Crystal Structure of mitochondrial...

New page

'''Unreleased structure'''

The entry 6cqo is ON HOLD

Authors: Singh, S.P., Kukshal, V., Bona, P.D., Lytle, A.K., Edwin, A., Galletto, R.

Description: Crystal Structure of mitochondrial single-stranded DNA binding proteins from S. cerevisiae (SeMet Labeled), Rim1 (Form2)
[[Category: Unreleased Structures]]
[[Category: Kukshal, V]]
[[Category: Lytle, A.K]]
[[Category: Bona, P.D]]
[[Category: Singh, S.P]]
[[Category: Edwin, A]]
[[Category: Galletto, R]]