1l1o - Revision history

OCA at 07:29, 14 February 2024

2024-02-14T07:29:28Z

←Older revision		Revision as of 07:29, 14 February 2024
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	<StructureSection load='1l1o' size='340' side='right'caption='[[1l1o]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='1l1o' size='340' side='right'caption='[[1l1o]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1l1o]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L1O OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1L1O FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1l1o]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L1O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1L1O FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.8Å</td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max~~-~~height: 3em;'>[[1jmc\|1jmc]]~~, [[~~1fgu~~\|~~1fgu]], [[1quq\|1quq]], [[1dpu\|1dpu~~]]~~</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>RFA3_HUMAN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~9606 HUMAN]), RFA2_HUMAN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=9606 HUMAN]), RFA1_HUMAN ([http~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])~~</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=1l1o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l1o OCA], [https://pdbe.org/1l1o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1l1o RCSB], [https://www.ebi.ac.uk/pdbsum/1l1o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1l1o 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=1l1o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l1o OCA], [~~http~~://pdbe.org/1l1o PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1l1o RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1l1o PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1l1o ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/RFA3_HUMAN RFA3_HUMAN]] Required for DNA recombination, repair and replication. The activity of RP-A is mediated by single-stranded DNA binding and protein interactions.<ref>PMID:19116208</ref> <ref>PMID:19996105</ref> Functions as component of the alternative replication protein A complex (aRPA). aRPA binds single-stranded DNA and probably plays a role in DNA repair; it does not support chromosomal DNA replication and cell cycle progression through S-phase. In vitro, aRPA cannot promote efficient priming by DNA polymerase alpha but supports DNA polymerase delta synthesis in the presence of PCNA and replication factor C (RFC), the dual incision/excision reaction of nucleotide excision repair and RAD51-dependent strand exchange.<ref>PMID:19116208</ref> <ref>PMID:19996105</ref> [[http://www.uniprot.org/uniprot/RFA1_HUMAN RFA1_HUMAN]] Plays an essential role in several cellular processes in DNA metabolism including replication, recombination and DNA repair. Binds and subsequently stabilizes single-stranded DNA intermediates and thus prevents complementary DNA from reannealing.<ref>PMID:19116208</ref> <ref>PMID:19996105</ref> Functions as component of the alternative replication protein A complex (aRPA). aRPA binds single-stranded DNA and probably plays a role in DNA repair; it does not support chromosomal DNA replication and cell cycle progression through S-phase. In vitro, aRPA cannot promote efficient priming by DNA polymerase alpha but supports DNA polymerase delta synthesis in the presence of PCNA and replication factor C (RFC), the dual incision/excision reaction of nucleotide excision repair and RAD51-dependent strand exchange.<ref>PMID:19116208</ref> <ref>PMID:19996105</ref> [[http://www.uniprot.org/uniprot/RFA2_HUMAN RFA2_HUMAN]] Required for DNA recombination, repair and replication. The activity of RP-A is mediated by single-stranded DNA binding and protein interactions. Required for the efficient recruitment of the DNA double-strand break repair factor RAD51 to chromatin in response to DNA damage.<ref>PMID:15205463</ref> <ref>PMID:19116208</ref> <ref>PMID:19996105</ref> <ref>PMID:20154705</ref> Functions as component of the alternative replication protein A complex (aRPA). aRPA binds single-stranded DNA and probably plays a role in DNA repair; it does not support chromosomal DNA replication and cell cycle progression through S-phase. In vitro, aRPA cannot promote efficient priming by DNA polymerase alpha but supports DNA polymerase delta synthesis in the presence of PCNA and replication factor C (RFC), the dual incision/excision reaction of nucleotide excision repair and RAD51-dependent strand exchange.<ref>PMID:15205463</ref> <ref>PMID:19116208</ref> <ref>PMID:19996105</ref> <ref>PMID:20154705</ref>	+	[https://www.uniprot.org/uniprot/RFA3_HUMAN RFA3_HUMAN] Required for DNA recombination, repair and replication. The activity of RP-A is mediated by single-stranded DNA binding and protein interactions.<ref>PMID:19116208</ref> <ref>PMID:19996105</ref> Functions as component of the alternative replication protein A complex (aRPA). aRPA binds single-stranded DNA and probably plays a role in DNA repair; it does not support chromosomal DNA replication and cell cycle progression through S-phase. In vitro, aRPA cannot promote efficient priming by DNA polymerase alpha but supports DNA polymerase delta synthesis in the presence of PCNA and replication factor C (RFC), the dual incision/excision reaction of nucleotide excision repair and RAD51-dependent strand exchange.<ref>PMID:19116208</ref> <ref>PMID:19996105</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1l1o ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1l1o ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The human single-stranded DNA-binding protein, replication protein A (RPA) binds DNA in at least two different modes: initial [8-10 nucleotides (nt)] and stable ( approximately 30 nt). Switching from 8 to 30 nt mode is associated with a large conformational change. Here we report the 2.8 A structure of the RPA trimerization core comprising the C-terminal DNA-binding domain of subunit RPA70 (DBD-C), the central DNA-binding domain of subunit RPA32 (DBD-D) and the entire RPA14 subunit. All three domains are built around a central oligonucleotide/oligosaccharide binding (OB)-fold and flanked by a helix at the C-terminus. Trimerization is mediated by three C-terminal helices arranged in parallel. The OB-fold of DBD-C possesses unique structural features; embedded zinc ribbon and helix-turn-helix motifs. Using time-resolved proteolysis with trypsin, we demonstrate that the trimerization core does not contribute to the binding with substrates of 10 nt, but interacts with oligonucleotides of 24 nt. Taken together, our data indicate that switching from 8-10 to 30 nt mode is mediated by DNA binding with the trimerization core.
-
-	Structure of the RPA trimerization core and its role in the multistep DNA-binding mechanism of RPA.,Bochkareva E, Korolev S, Lees-Miller SP, Bochkarev A EMBO J. 2002 Apr 2;21(7):1855-63. PMID:11927569<ref>PMID:11927569</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1l1o" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Bochkarev, A]]	+	[[Category: Bochkarev A]]
-	[[Category: Bochkareva~~, E V~~]]	+	[[Category: Bochkareva EV]]
-	[[Category: Korolev, S]]	+	[[Category: Korolev S]]
-	[[Category: Lees-Miller~~, S P]]~~	+	[[Category: Lees-Miller SP]]
-	~~[[Category: Dna binding protein]]~~	+
-	~~[[Category: Eukaryotic ssb]]~~	+
-	~~[[Category: Ob-fold]]~~	+
-	~~[[Category: Ssdna binding protein~~]]	+

OCA at 07:53, 25 November 2020

2020-11-25T07:53:43Z

←Older revision		Revision as of 07:53, 25 November 2020
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	==Structure of the human Replication Protein A (RPA) trimerization core==		==Structure of the human Replication Protein A (RPA) trimerization core==
-	<StructureSection load='1l1o' size='340' side='right' caption='[[1l1o]], [[Resolution\|resolution]] 2.80Å' scene=''>	+	<StructureSection load='1l1o' size='340' side='right'caption='[[1l1o]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1l1o]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L1O OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1L1O FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1l1o]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L1O OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1L1O FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1jmc\|1jmc]], [[1fgu\|1fgu]], [[1quq\|1quq]], [[1dpu\|1dpu]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1jmc\|1jmc]], [[1fgu\|1fgu]], [[1quq\|1quq]], [[1dpu\|1dpu]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RFA3_HUMAN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), RFA2_HUMAN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), RFA1_HUMAN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RFA3_HUMAN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), RFA2_HUMAN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), RFA1_HUMAN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=1l1o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l1o OCA], [http://pdbe.org/1l1o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1l1o RCSB], [http://www.ebi.ac.uk/pdbsum/1l1o PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1l1o 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=1l1o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l1o OCA], [http://pdbe.org/1l1o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1l1o RCSB], [http://www.ebi.ac.uk/pdbsum/1l1o PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1l1o ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	</div>		</div>
	<div class="pdbe-citations 1l1o" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1l1o" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Single-stranded DNA-binding protein 3D structures\|Single-stranded DNA-binding protein 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Bochkarev, A]]		[[Category: Bochkarev, A]]
	[[Category: Bochkareva, E V]]		[[Category: Bochkareva, E V]]

OCA at 21:29, 24 January 2018

2018-01-24T21:29:31Z

←Older revision		Revision as of 21:29, 24 January 2018
Line 1:		Line 1:
		+
	==Structure of the human Replication Protein A (RPA) trimerization core==		==Structure of the human Replication Protein A (RPA) trimerization core==
	<StructureSection load='1l1o' size='340' side='right' caption='[[1l1o]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='1l1o' size='340' side='right' caption='[[1l1o]], [[Resolution\|resolution]] 2.80Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1jmc\|1jmc]], [[1fgu\|1fgu]], [[1quq\|1quq]], [[1dpu\|1dpu]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1jmc\|1jmc]], [[1fgu\|1fgu]], [[1quq\|1quq]], [[1dpu\|1dpu]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RFA3_HUMAN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), RFA2_HUMAN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), RFA1_HUMAN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RFA3_HUMAN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), RFA2_HUMAN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), RFA1_HUMAN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=1l1o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l1o OCA], [http://pdbe.org/1l1o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1l1o RCSB], [http://www.ebi.ac.uk/pdbsum/1l1o PDBsum]</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=1l1o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l1o OCA], [http://pdbe.org/1l1o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1l1o RCSB], [http://www.ebi.ac.uk/pdbsum/1l1o PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1l1o ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/l1/1l1o_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/l1/1l1o_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 29:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 1l1o" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1l1o" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Single-stranded DNA-binding protein\|Single-stranded DNA-binding protein]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 01:08, 9 February 2016

2016-02-09T01:08:25Z

←Older revision		Revision as of 01:08, 9 February 2016
Line 18:		Line 18:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1l1o ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 17:08, 10 September 2015

2015-09-10T17:08:11Z

←Older revision		Revision as of 17:08, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1l1o' size='340' side='right' caption='[[1l1o]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='1l1o' size='340' side='right' caption='[[1l1o]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1l1o]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Homo_sapiens Homo sapiens~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L1O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1L1O FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1l1o]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L1O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1L1O FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><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=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1jmc\|1jmc]], [[1fgu\|1fgu]], [[1quq\|1quq]], [[1dpu\|1dpu]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1jmc\|1jmc]], [[1fgu\|1fgu]], [[1quq\|1quq]], [[1dpu\|1dpu]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RFA3_HUMAN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 ~~Homo sapiens~~]), RFA2_HUMAN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 ~~Homo sapiens~~]), RFA1_HUMAN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 ~~Homo sapiens~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RFA3_HUMAN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), RFA2_HUMAN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), RFA1_HUMAN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=1l1o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l1o OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1l1o RCSB], [http://www.ebi.ac.uk/pdbsum/1l1o PDBsum]</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=1l1o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l1o OCA], [http://pdbe.org/1l1o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1l1o RCSB], [http://www.ebi.ac.uk/pdbsum/1l1o PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 28:		Line 28:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 1l1o" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Bochkarev, A]]		[[Category: Bochkarev, A]]
	[[Category: Bochkareva, E V]]		[[Category: Bochkareva, E V]]

OCA at 03:23, 25 December 2014

2014-12-25T03:23:46Z

←Older revision		Revision as of 03:23, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1l1o]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L1O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1L1O FirstGlance]. <br>		<table><tr><td colspan='2'>[[1l1o]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L1O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1L1O FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1jmc\|1jmc]], [[1fgu\|1fgu]], [[1quq\|1quq]], [[1dpu\|1dpu]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1jmc\|1jmc]], [[1fgu\|1fgu]], [[1quq\|1quq]], [[1dpu\|1dpu]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RFA3_HUMAN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]), RFA2_HUMAN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]), RFA1_HUMAN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RFA3_HUMAN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]), RFA2_HUMAN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]), RFA1_HUMAN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1l1o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l1o OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1l1o RCSB], [http://www.ebi.ac.uk/pdbsum/1l1o PDBsum]</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=1l1o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l1o OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1l1o RCSB], [http://www.ebi.ac.uk/pdbsum/1l1o PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RFA3_HUMAN RFA3_HUMAN]] Required for DNA recombination, repair and replication. The activity of RP-A is mediated by single-stranded DNA binding and protein interactions.<ref>PMID:19116208</ref> <ref>PMID:19996105</ref> Functions as component of the alternative replication protein A complex (aRPA). aRPA binds single-stranded DNA and probably plays a role in DNA repair; it does not support chromosomal DNA replication and cell cycle progression through S-phase. In vitro, aRPA cannot promote efficient priming by DNA polymerase alpha but supports DNA polymerase delta synthesis in the presence of PCNA and replication factor C (RFC), the dual incision/excision reaction of nucleotide excision repair and RAD51-dependent strand exchange.<ref>PMID:19116208</ref> <ref>PMID:19996105</ref> [[http://www.uniprot.org/uniprot/RFA1_HUMAN RFA1_HUMAN]] Plays an essential role in several cellular processes in DNA metabolism including replication, recombination and DNA repair. Binds and subsequently stabilizes single-stranded DNA intermediates and thus prevents complementary DNA from reannealing.<ref>PMID:19116208</ref> <ref>PMID:19996105</ref> Functions as component of the alternative replication protein A complex (aRPA). aRPA binds single-stranded DNA and probably plays a role in DNA repair; it does not support chromosomal DNA replication and cell cycle progression through S-phase. In vitro, aRPA cannot promote efficient priming by DNA polymerase alpha but supports DNA polymerase delta synthesis in the presence of PCNA and replication factor C (RFC), the dual incision/excision reaction of nucleotide excision repair and RAD51-dependent strand exchange.<ref>PMID:19116208</ref> <ref>PMID:19996105</ref> [[http://www.uniprot.org/uniprot/RFA2_HUMAN RFA2_HUMAN]] Required for DNA recombination, repair and replication. The activity of RP-A is mediated by single-stranded DNA binding and protein interactions. Required for the efficient recruitment of the DNA double-strand break repair factor RAD51 to chromatin in response to DNA damage.<ref>PMID:15205463</ref> <ref>PMID:19116208</ref> <ref>PMID:19996105</ref> <ref>PMID:20154705</ref> Functions as component of the alternative replication protein A complex (aRPA). aRPA binds single-stranded DNA and probably plays a role in DNA repair; it does not support chromosomal DNA replication and cell cycle progression through S-phase. In vitro, aRPA cannot promote efficient priming by DNA polymerase alpha but supports DNA polymerase delta synthesis in the presence of PCNA and replication factor C (RFC), the dual incision/excision reaction of nucleotide excision repair and RAD51-dependent strand exchange.<ref>PMID:15205463</ref> <ref>PMID:19116208</ref> <ref>PMID:19996105</ref> <ref>PMID:20154705</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 36:
	</StructureSection>		</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Bochkarev, A.]]	+	[[Category: Bochkarev, A]]
-	[[Category: Bochkareva, E V.]]	+	[[Category: Bochkareva, E V]]
-	[[Category: Korolev, S.]]	+	[[Category: Korolev, S]]
-	[[Category: Lees-Miller, S P.]]	+	[[Category: Lees-Miller, S P]]
	[[Category: Dna binding protein]]		[[Category: Dna binding protein]]
	[[Category: Eukaryotic ssb]]		[[Category: Eukaryotic ssb]]
	[[Category: Ob-fold]]		[[Category: Ob-fold]]
	[[Category: Ssdna binding protein]]		[[Category: Ssdna binding protein]]

OCA at 13:50, 28 September 2014

2014-09-28T13:50:57Z

←Older revision		Revision as of 13:50, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1l1o.~~png~~\|~~left~~\|200px]]	+	==Structure of the human Replication Protein A (RPA) trimerization core==
		+	<StructureSection load='1l1o' size='340' side='right' caption='[[1l1o]], [[Resolution\|resolution]] 2.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1l1o]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L1O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1L1O FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1jmc\|1jmc]], [[1fgu\|1fgu]], [[1quq\|1quq]], [[1dpu\|1dpu]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RFA3_HUMAN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]), RFA2_HUMAN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]), RFA1_HUMAN ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1l1o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l1o OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1l1o RCSB], [http://www.ebi.ac.uk/pdbsum/1l1o PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/l1/1l1o_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The human single-stranded DNA-binding protein, replication protein A (RPA) binds DNA in at least two different modes: initial [8-10 nucleotides (nt)] and stable ( approximately 30 nt). Switching from 8 to 30 nt mode is associated with a large conformational change. Here we report the 2.8 A structure of the RPA trimerization core comprising the C-terminal DNA-binding domain of subunit RPA70 (DBD-C), the central DNA-binding domain of subunit RPA32 (DBD-D) and the entire RPA14 subunit. All three domains are built around a central oligonucleotide/oligosaccharide binding (OB)-fold and flanked by a helix at the C-terminus. Trimerization is mediated by three C-terminal helices arranged in parallel. The OB-fold of DBD-C possesses unique structural features; embedded zinc ribbon and helix-turn-helix motifs. Using time-resolved proteolysis with trypsin, we demonstrate that the trimerization core does not contribute to the binding with substrates of 10 nt, but interacts with oligonucleotides of 24 nt. Taken together, our data indicate that switching from 8-10 to 30 nt mode is mediated by DNA binding with the trimerization core.

-	~~{{STRUCTURE_1l1o\| PDB=1l1o \| SCENE= }}~~	+	Structure of the RPA trimerization core and its role in the multistep DNA-binding mechanism of RPA.,Bochkareva E, Korolev S, Lees-Miller SP, Bochkarev A EMBO J. 2002 Apr 2;21(7):1855-63. PMID:11927569<ref>PMID:11927569</ref>

-	~~===Structure~~ of the ~~human Replication Protein A (RPA) trimerization core===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-	~~{{ABSTRACT_PUBMED_11927569}}~~	+	==See Also==
-		+	*[[Single-stranded DNA-binding protein\|Single-stranded DNA-binding protein]]
-	==~~About this Structure~~==	+	== References ==
-	[[~~1l1o~~]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L1O OCA].	+	<references/>
-		+	__TOC__
-	==~~Reference~~==	+	</StructureSection>
-	<~~ref group="xtra">PMID:011927569<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Bochkarev, A.]]		[[Category: Bochkarev, A.]]

OCA: Protected "1l1o" [edit=sysop:move=sysop]

2012-12-05T20:58:29Z

Protected "1l1o" [edit=sysop:move=sysop]

←Older revision

Revision as of 20:58, 5 December 2012

OCA at 20:58, 5 December 2012

2012-12-05T20:58:25Z

←Older revision		Revision as of 20:58, 5 December 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1l1o.png\|left\|200px]]		[[Image:1l1o.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1l1o", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_1l1o\| PDB=1l1o \| SCENE= }}		{{STRUCTURE_1l1o\| PDB=1l1o \| SCENE= }}

	===Structure of the human Replication Protein A (RPA) trimerization core===		===Structure of the human Replication Protein A (RPA) trimerization core===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_11927569}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 11927569 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_11927569}}		{{ABSTRACT_PUBMED_11927569}}

	==About this Structure==		==About this Structure==
-	~~1L1O~~ is a 6 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L1O OCA].	+	[[1l1o]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L1O OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~11927569~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:011927569</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Bochkarev, A.]]		[[Category: Bochkarev, A.]]
Line 29:		Line 17:
	[[Category: Korolev, S.]]		[[Category: Korolev, S.]]
	[[Category: Lees-Miller, S P.]]		[[Category: Lees-Miller, S P.]]
		+	[[Category: Dna binding protein]]
	[[Category: Eukaryotic ssb]]		[[Category: Eukaryotic ssb]]
	[[Category: Ob-fold]]		[[Category: Ob-fold]]
	[[Category: Ssdna binding protein]]		[[Category: Ssdna binding protein]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 05:14:06 2009''

OCA at 03:14, 17 February 2009

2009-02-17T03:14:10Z

←Older revision		Revision as of 03:14, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	1L1O is a ~~[[Protein complex]]~~ structure of sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L1O OCA].	+	1L1O is a 6 chains structure of sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L1O OCA].

	==Reference==		==Reference==
-	~~Structure of the RPA trimerization core and its role in the multistep DNA-binding mechanism of RPA., Bochkareva E, Korolev S, Lees-Miller SP, Bochkarev A, EMBO J. 2002 Apr 2;21(7):1855-63.~~ PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/11927569 11927569]~~	+	<ref group="xtra">PMID:11927569</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Protein complex]]
	[[Category: Bochkarev, A.]]		[[Category: Bochkarev, A.]]
	[[Category: Bochkareva, E V.]]		[[Category: Bochkareva, E V.]]
Line 34:		Line 33:
	[[Category: Ssdna binding protein]]		[[Category: Ssdna binding protein]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Wed Jul 2 11~~:30:~~16 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 05:14:06 2009''