5omb - Revision history

OCA at 16:54, 13 December 2023

OCA — Wed, 13 Dec 2023 16:54:33 GMT

←Older revision		Revision as of 16:54, 13 December 2023
Line 3:		Line 3:
	<StructureSection load='5omb' size='340' side='right'caption='[[5omb]], [[Resolution\|resolution]] 1.94Å' scene=''>		<StructureSection load='5omb' size='340' side='right'caption='[[5omb]], [[Resolution\|resolution]] 1.94Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5omb]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OMB OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5OMB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5omb]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Kluyveromyces_lactis_NRRL_Y-1140 Kluyveromyces lactis NRRL Y-1140] and [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=5OMB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5OMB FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>~~, ~~<scene name='pdbligand=EDO:~~1~~,2-ETHANEDIOL'>EDO</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]] 1.94Å</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='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></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=5omb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5omb OCA], [~~http~~://pdbe.org/5omb PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5omb RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5omb PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5omb 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=5omb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5omb OCA], [https://pdbe.org/5omb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5omb RCSB], [https://www.ebi.ac.uk/pdbsum/5omb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5omb ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/RFA1_YEAST RFA1_YEAST]] Binds to single-stranded sequences participating in DNA replication in addition to those mediating transcriptional repression (URS1) and activation (CAR1). Stimulates the activity of a cognate strand exchange protein (SEP1). It cooperates with T-AG and DNA topoisomerase I to unwind template DNA containing the simian virus 40 origin of DNA replication. [[http://www.uniprot.org/uniprot/LCD1_KLULA LCD1_KLULA]] Forms a complex with the serine/threonine kinase MEC1 which activates checkpoint signaling upon genotoxic stresses. The MEC1-LCD1 complex is recruited to DNA lesions in order to initiates the DNA repair by homologous recombination. Required for cell growth and meiotic recombination (By similarity).	+	[https://www.uniprot.org/uniprot/RFA1_YEAST RFA1_YEAST] Binds to single-stranded sequences participating in DNA replication in addition to those mediating transcriptional repression (URS1) and activation (CAR1). Stimulates the activity of a cognate strand exchange protein (SEP1). It cooperates with T-AG and DNA topoisomerase I to unwind template DNA containing the simian virus 40 origin of DNA replication.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 23:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Kluyveromyces lactis NRRL Y-1140]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Deshpande, I]]	+	[[Category: Saccharomyces cerevisiae S288C]]
-	[[Category: Gasser~~, S M~~]]	+	[[Category: Deshpande I]]
-	[[Category: Gut, H]]	+	[[Category: Gasser SM]]
-	[[Category: Keusch~~, J J~~]]	+	[[Category: Gut H]]
-	[[Category: Seeber, A]]	+	[[Category: Keusch JJ]]
-	[[Category: Shimada, K]]	+	[[Category: Seeber A]]
-	~~[[Category: Coiled-coil domain]]~~	+	[[Category: Shimada K]]
-	~~[[Category: Complex]]~~	+
-	~~[[Category: Nucleus]]~~	+
-	~~[[Category: Oligonucleotide-binding fold]]~~	+
-	~~[[Category: Protein binding~~]]	+

OCA at 07:28, 2 September 2020

OCA — Wed, 02 Sep 2020 07:28:49 GMT

←Older revision		Revision as of 07:28, 2 September 2020
Line 1:		Line 1:

	==Crystal structure of K. lactis Ddc2 N-terminus in complex with S. cerevisiae Rfa1 N-OB domain==		==Crystal structure of K. lactis Ddc2 N-terminus in complex with S. cerevisiae Rfa1 N-OB domain==
-	<StructureSection load='5omb' size='340' side='right' caption='[[5omb]], [[Resolution\|resolution]] 1.94Å' scene=''>	+	<StructureSection load='5omb' size='340' side='right'caption='[[5omb]], [[Resolution\|resolution]] 1.94Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5omb]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OMB OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5OMB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5omb]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OMB OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5OMB FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></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='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='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=5omb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5omb OCA], [http://pdbe.org/5omb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5omb RCSB], [http://www.ebi.ac.uk/pdbsum/5omb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5omb 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=5omb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5omb OCA], [http://pdbe.org/5omb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5omb RCSB], [http://www.ebi.ac.uk/pdbsum/5omb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5omb ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 23:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Deshpande, I]]		[[Category: Deshpande, I]]
	[[Category: Gasser, S M]]		[[Category: Gasser, S M]]

OCA at 07:04, 25 October 2017

OCA — Wed, 25 Oct 2017 07:04:02 GMT

←Older revision		Revision as of 07:04, 25 October 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5omb is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of K. lactis Ddc2 N-terminus in complex with S. cerevisiae Rfa1 N-OB domain==
		+	<StructureSection load='5omb' size='340' side='right' caption='[[5omb]], [[Resolution\|resolution]] 1.94Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5omb]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OMB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OMB FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene></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='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=5omb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5omb OCA], [http://pdbe.org/5omb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5omb RCSB], [http://www.ebi.ac.uk/pdbsum/5omb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5omb ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RFA1_YEAST RFA1_YEAST]] Binds to single-stranded sequences participating in DNA replication in addition to those mediating transcriptional repression (URS1) and activation (CAR1). Stimulates the activity of a cognate strand exchange protein (SEP1). It cooperates with T-AG and DNA topoisomerase I to unwind template DNA containing the simian virus 40 origin of DNA replication. [[http://www.uniprot.org/uniprot/LCD1_KLULA LCD1_KLULA]] Forms a complex with the serine/threonine kinase MEC1 which activates checkpoint signaling upon genotoxic stresses. The MEC1-LCD1 complex is recruited to DNA lesions in order to initiates the DNA repair by homologous recombination. Required for cell growth and meiotic recombination (By similarity).
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Mec1-Ddc2 (ATR-ATRIP) is a key DNA-damage-sensing kinase that is recruited through the single-stranded (ss) DNA-binding replication protein A (RPA) to initiate the DNA damage checkpoint response. Activation of ATR-ATRIP in the absence of DNA damage is lethal. Therefore, it is important that damage-specific recruitment precedes kinase activation, which is achieved at least in part by Mec1-Ddc2 homodimerization. Here, we report a structural, biochemical, and functional characterization of the yeast Mec1-Ddc2-RPA assembly. High-resolution co-crystal structures of Ddc2-Rfa1 and Ddc2-Rfa1-t11 (K45E mutant) N termini and of the Ddc2 coiled-coil domain (CCD) provide insight into Mec1-Ddc2 homodimerization and damage-site targeting. Based on our structural and functional findings, we present a Mec1-Ddc2-RPA-ssDNA composite structural model. By way of validation, we show that RPA-dependent recruitment of Mec1-Ddc2 is crucial for maintaining its homodimeric state at ssDNA and that Ddc2's recruitment domain and CCD are important for Mec1-dependent survival of UV-light-induced DNA damage.

-	~~Authors~~:	+	Structural Basis of Mec1-Ddc2-RPA Assembly and Activation on Single-Stranded DNA at Sites of Damage.,Deshpande I, Seeber A, Shimada K, Keusch JJ, Gut H, Gasser SM Mol Cell. 2017 Oct 19;68(2):431-445.e5. doi: 10.1016/j.molcel.2017.09.019. Epub, 2017 Oct 12. PMID:29033322<ref>PMID:29033322</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5omb" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Deshpande, I]]
		+	[[Category: Gasser, S M]]
		+	[[Category: Gut, H]]
		+	[[Category: Keusch, J J]]
		+	[[Category: Seeber, A]]
		+	[[Category: Shimada, K]]
		+	[[Category: Coiled-coil domain]]
		+	[[Category: Complex]]
		+	[[Category: Nucleus]]
		+	[[Category: Oligonucleotide-binding fold]]
		+	[[Category: Protein binding]]

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

OCA — Wed, 27 Sep 2017 12:35:15 GMT

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

←Older revision

Revision as of 12:35, 27 September 2017

OCA: New page: '''Unreleased structure''' The entry 5omb is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

OCA — Wed, 27 Sep 2017 12:35:14 GMT

New page: '''Unreleased structure''' The entry 5omb is ON HOLD until Paper Publication Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5omb is ON HOLD until Paper Publication

Authors:

Description:
[[Category: Unreleased Structures]]