1pa6 - Revision history

OCA at 08:06, 14 February 2024

OCA — Wed, 14 Feb 2024 08:06:26 GMT

←Older revision		Revision as of 08:06, 14 February 2024
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	<StructureSection load='1pa6' size='340' side='right'caption='[[1pa6]], [[Resolution\|resolution]] 2.45Å' scene=''>		<StructureSection load='1pa6' size='340' side='right'caption='[[1pa6]], [[Resolution\|resolution]] 2.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1pa6]] is a 5 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Ciliate Ciliate~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PA6 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1PA6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1pa6]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Sterkiella_nova Sterkiella nova]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PA6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PA6 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=NA:SODIUM+ION'>NA</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]] 2.45Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>[[1otc\|1otc]], [[1jb7\|1jb7]], [[1kix\|1kix]], [[1k8g\|1k8g]], [[1ph1\|1ph1]], [[1ph2\|1ph2]], [[1ph3\|1ph3]], [[1ph4\|1ph4]], [[1ph5\|1ph5]], [[1ph6\|1ph6]], [[1ph7\|1ph7]], [[1ph8\|1ph8]], [[1ph9\|1ph9]], [[1phj\|1phj]]</~~div~~><~~/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=NA:SODIUM+ION'>NA</scene></td></tr>
-	~~<tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td><td class="sblockDat">MAC-56A AND MAC-56K AND MAC-56S ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=200597 Ciliate]), MAC-41A AND MAC-41S ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=200597 Ciliate])</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=1pa6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pa6 OCA], [https://pdbe.org/1pa6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pa6 RCSB], [https://www.ebi.ac.uk/pdbsum/1pa6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pa6 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=1pa6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pa6 OCA], [~~http~~://pdbe.org/1pa6 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1pa6 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1pa6 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1pa6 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/TEBB_OXYNO TEBB_OXYNO]] May function as protective capping of the single-stranded telomeric overhang. May also participate in telomere length regulation during DNA replication. Binds specifically to the T4G4-containing extension on the 3'strand and protects this region of the telomere from nuclease digestion and chemical modification. [[http://www.uniprot.org/uniprot/TEBA_OXYNO TEBA_OXYNO]] May function as protective capping of the single-stranded telomeric overhang. May also participate in telomere length regulation during DNA replication. Binds specifically to the T4G4-containing extension on the 3'strand and protects this region of the telomere from nuclease digestion and chemical modification.	+	[https://www.uniprot.org/uniprot/TEBA_STENO TEBA_STENO] May function as protective capping of the single-stranded telomeric overhang. May also participate in telomere length regulation during DNA replication. Binds specifically to the T4G4-containing extension on the 3'strand and protects this region of the telomere from nuclease digestion and chemical modification.
	== 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=1pa6 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=1pa6 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Sequence-specific protein recognition of single-stranded nucleic acids is critical for many fundamental cellular processes, such as DNA replication, DNA repair, transcription, translation, recombination, apoptosis and telomere maintenance. To explore the mechanisms of sequence-specific ssDNA recognition, we determined the crystal structures of 10 different non-cognate ssDNAs complexed with the Oxytricha nova telomere end-binding protein (OnTEBP) and evaluated their corresponding binding affinities (PDB ID codes 1PH1-1PH9 and 1PHJ). The thermodynamic and structural effects of these sequence perturbations could not have been predicted based solely upon the cognate structure. OnTEBP accommodates non-cognate nucleotides by both subtle adjustments and surprisingly large structural rearrangements in the ssDNA. In two complexes containing ssDNA intermediates that occur during telomere extension by telomerase, entire nucleotides are expelled from the complex. Concurrently, the sequence register of the ssDNA shifts to re-establish a more cognate-like pattern. This phenomenon, termed nucleotide shuffling, may be of general importance in protein recognition of single-stranded nucleic acids. This set of structural and thermodynamic data highlights a fundamental difference between protein recognition of ssDNA versus dsDNA.
-
-	Nucleotide shuffling and ssDNA recognition in Oxytricha nova telomere end-binding protein complexes.,Theobald DL, Schultz SC EMBO J. 2003 Aug 15;22(16):4314-24. PMID:12912928<ref>PMID:12912928</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1pa6" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Ciliate]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Schultz, S C~~]]	+	[[Category: Sterkiella nova]]
-	[[Category: ~~Theobald, D L~~]]	+	[[Category: Schultz SC]]
-	[[Category: ~~Dna binding protein-dna complex]]~~	+	[[Category: Theobald DL]]
-	~~[[Category: Noncognate]]~~	+
-	~~[[Category: Ob fold]]~~	+
-	~~[[Category: Oligonucleotide and oligosaccharide binding fold]]~~	+
-	~~[[Category: Protein dna interaction]]~~	+
-	~~[[Category: Protein/dna]]~~	+
-	~~[[Category: Sequence specificity]]~~	+
-	~~[[Category: Single strand dna binding protein]]~~	+
-	~~[[Category: Telomere~~]]	+

OCA at 07:27, 9 December 2020

OCA — Wed, 09 Dec 2020 07:27:01 GMT

←Older revision		Revision as of 07:27, 9 December 2020
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	==Crystal structure of the OXYTRICHA nova telomere end-binding protein complexed with noncognate ssDNA GGGGTTTTGAGG==		==Crystal structure of the OXYTRICHA nova telomere end-binding protein complexed with noncognate ssDNA GGGGTTTTGAGG==
-	<StructureSection load='1pa6' size='340' side='right' caption='[[1pa6]], [[Resolution\|resolution]] 2.45Å' scene=''>	+	<StructureSection load='1pa6' size='340' side='right'caption='[[1pa6]], [[Resolution\|resolution]] 2.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1pa6]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Ciliate Ciliate]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PA6 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1PA6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1pa6]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Ciliate Ciliate]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PA6 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1PA6 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=NA:SODIUM+ION'>NA</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=NA:SODIUM+ION'>NA</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1otc\|1otc]], [[1jb7\|1jb7]], [[1kix\|1kix]], [[1k8g\|1k8g]], [[1ph1\|1ph1]], [[1ph2\|1ph2]], [[1ph3\|1ph3]], [[1ph4\|1ph4]], [[1ph5\|1ph5]], [[1ph6\|1ph6]], [[1ph7\|1ph7]], [[1ph8\|1ph8]], [[1ph9\|1ph9]], [[1phj\|1phj]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1otc\|1otc]], [[1jb7\|1jb7]], [[1kix\|1kix]], [[1k8g\|1k8g]], [[1ph1\|1ph1]], [[1ph2\|1ph2]], [[1ph3\|1ph3]], [[1ph4\|1ph4]], [[1ph5\|1ph5]], [[1ph6\|1ph6]], [[1ph7\|1ph7]], [[1ph8\|1ph8]], [[1ph9\|1ph9]], [[1phj\|1phj]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MAC-56A AND MAC-56K AND MAC-56S ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=200597 Ciliate]), MAC-41A AND MAC-41S ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=200597 Ciliate])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MAC-56A AND MAC-56K AND MAC-56S ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=200597 Ciliate]), MAC-41A AND MAC-41S ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=200597 Ciliate])</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=1pa6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pa6 OCA], [http://pdbe.org/1pa6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1pa6 RCSB], [http://www.ebi.ac.uk/pdbsum/1pa6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1pa6 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=1pa6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pa6 OCA], [http://pdbe.org/1pa6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1pa6 RCSB], [http://www.ebi.ac.uk/pdbsum/1pa6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1pa6 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	</StructureSection>		</StructureSection>
	[[Category: Ciliate]]		[[Category: Ciliate]]
		+	[[Category: Large Structures]]
	[[Category: Schultz, S C]]		[[Category: Schultz, S C]]
	[[Category: Theobald, D L]]		[[Category: Theobald, D L]]

OCA at 07:58, 15 February 2018

OCA — Thu, 15 Feb 2018 07:58:19 GMT

←Older revision		Revision as of 07:58, 15 February 2018
Line 1:		Line 1:
		+
	==Crystal structure of the OXYTRICHA nova telomere end-binding protein complexed with noncognate ssDNA GGGGTTTTGAGG==		==Crystal structure of the OXYTRICHA nova telomere end-binding protein complexed with noncognate ssDNA GGGGTTTTGAGG==
	<StructureSection load='1pa6' size='340' side='right' caption='[[1pa6]], [[Resolution\|resolution]] 2.45Å' scene=''>		<StructureSection load='1pa6' size='340' side='right' caption='[[1pa6]], [[Resolution\|resolution]] 2.45Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1otc\|1otc]], [[1jb7\|1jb7]], [[1kix\|1kix]], [[1k8g\|1k8g]], [[1ph1\|1ph1]], [[1ph2\|1ph2]], [[1ph3\|1ph3]], [[1ph4\|1ph4]], [[1ph5\|1ph5]], [[1ph6\|1ph6]], [[1ph7\|1ph7]], [[1ph8\|1ph8]], [[1ph9\|1ph9]], [[1phj\|1phj]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1otc\|1otc]], [[1jb7\|1jb7]], [[1kix\|1kix]], [[1k8g\|1k8g]], [[1ph1\|1ph1]], [[1ph2\|1ph2]], [[1ph3\|1ph3]], [[1ph4\|1ph4]], [[1ph5\|1ph5]], [[1ph6\|1ph6]], [[1ph7\|1ph7]], [[1ph8\|1ph8]], [[1ph9\|1ph9]], [[1phj\|1phj]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MAC-56A AND MAC-56K AND MAC-56S ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=200597 Ciliate]), MAC-41A AND MAC-41S ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=200597 Ciliate])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MAC-56A AND MAC-56K AND MAC-56S ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=200597 Ciliate]), MAC-41A AND MAC-41S ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=200597 Ciliate])</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=1pa6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pa6 OCA], [http://pdbe.org/1pa6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1pa6 RCSB], [http://www.ebi.ac.uk/pdbsum/1pa6 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=1pa6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pa6 OCA], [http://pdbe.org/1pa6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1pa6 RCSB], [http://www.ebi.ac.uk/pdbsum/1pa6 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1pa6 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pa/1pa6_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pa/1pa6_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>
	</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=1pa6 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 01:54, 12 September 2015

OCA — Sat, 12 Sep 2015 01:54:07 GMT

←Older revision		Revision as of 01:54, 12 September 2015
Line 2:		Line 2:
	<StructureSection load='1pa6' size='340' side='right' caption='[[1pa6]], [[Resolution\|resolution]] 2.45Å' scene=''>		<StructureSection load='1pa6' size='340' side='right' caption='[[1pa6]], [[Resolution\|resolution]] 2.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1pa6]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Sterkiella_nova Sterkiella nova~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PA6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PA6 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1pa6]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Ciliate Ciliate]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PA6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PA6 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=NA:SODIUM+ION'>NA</scene></td></tr>		</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=NA:SODIUM+ION'>NA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1otc\|1otc]], [[1jb7\|1jb7]], [[1kix\|1kix]], [[1k8g\|1k8g]], [[1ph1\|1ph1]], [[1ph2\|1ph2]], [[1ph3\|1ph3]], [[1ph4\|1ph4]], [[1ph5\|1ph5]], [[1ph6\|1ph6]], [[1ph7\|1ph7]], [[1ph8\|1ph8]], [[1ph9\|1ph9]], [[1phj\|1phj]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1otc\|1otc]], [[1jb7\|1jb7]], [[1kix\|1kix]], [[1k8g\|1k8g]], [[1ph1\|1ph1]], [[1ph2\|1ph2]], [[1ph3\|1ph3]], [[1ph4\|1ph4]], [[1ph5\|1ph5]], [[1ph6\|1ph6]], [[1ph7\|1ph7]], [[1ph8\|1ph8]], [[1ph9\|1ph9]], [[1phj\|1phj]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MAC-56A AND MAC-56K AND MAC-56S ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=200597 ~~Sterkiella nova~~]), MAC-41A AND MAC-41S ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=200597 ~~Sterkiella nova~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MAC-56A AND MAC-56K AND MAC-56S ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=200597 Ciliate]), MAC-41A AND MAC-41S ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=200597 Ciliate])</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=1pa6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pa6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1pa6 RCSB], [http://www.ebi.ac.uk/pdbsum/1pa6 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=1pa6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pa6 OCA], [http://pdbe.org/1pa6 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1pa6 RCSB], [http://www.ebi.ac.uk/pdbsum/1pa6 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 1pa6" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Sterkiella nova~~]]	+	[[Category: Ciliate]]
	[[Category: Schultz, S C]]		[[Category: Schultz, S C]]
	[[Category: Theobald, D L]]		[[Category: Theobald, D L]]

OCA at 22:18, 25 December 2014

OCA — Thu, 25 Dec 2014 22:18:10 GMT

←Older revision		Revision as of 22:18, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1pa6]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Sterkiella_nova Sterkiella nova]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PA6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PA6 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1pa6]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Sterkiella_nova Sterkiella nova]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PA6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PA6 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene><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=NA:SODIUM+ION'>NA</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1otc\|1otc]], [[1jb7\|1jb7]], [[1kix\|1kix]], [[1k8g\|1k8g]], [[1ph1\|1ph1]], [[1ph2\|1ph2]], [[1ph3\|1ph3]], [[1ph4\|1ph4]], [[1ph5\|1ph5]], [[1ph6\|1ph6]], [[1ph7\|1ph7]], [[1ph8\|1ph8]], [[1ph9\|1ph9]], [[1phj\|1phj]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1otc\|1otc]], [[1jb7\|1jb7]], [[1kix\|1kix]], [[1k8g\|1k8g]], [[1ph1\|1ph1]], [[1ph2\|1ph2]], [[1ph3\|1ph3]], [[1ph4\|1ph4]], [[1ph5\|1ph5]], [[1ph6\|1ph6]], [[1ph7\|1ph7]], [[1ph8\|1ph8]], [[1ph9\|1ph9]], [[1phj\|1phj]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MAC-56A AND MAC-56K AND MAC-56S ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=200597 Sterkiella nova]), MAC-41A AND MAC-41S ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=200597 Sterkiella nova])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MAC-56A AND MAC-56K AND MAC-56S ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=200597 Sterkiella nova]), MAC-41A AND MAC-41S ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=200597 Sterkiella nova])</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=1pa6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pa6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1pa6 RCSB], [http://www.ebi.ac.uk/pdbsum/1pa6 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=1pa6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pa6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1pa6 RCSB], [http://www.ebi.ac.uk/pdbsum/1pa6 PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/TEBB_OXYNO TEBB_OXYNO]] May function as protective capping of the single-stranded telomeric overhang. May also participate in telomere length regulation during DNA replication. Binds specifically to the T4G4-containing extension on the 3'strand and protects this region of the telomere from nuclease digestion and chemical modification. [[http://www.uniprot.org/uniprot/TEBA_OXYNO TEBA_OXYNO]] May function as protective capping of the single-stranded telomeric overhang. May also participate in telomere length regulation during DNA replication. Binds specifically to the T4G4-containing extension on the 3'strand and protects this region of the telomere from nuclease digestion and chemical modification.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</StructureSection>		</StructureSection>
	[[Category: Sterkiella nova]]		[[Category: Sterkiella nova]]
-	[[Category: Schultz, S C.]]	+	[[Category: Schultz, S C]]
-	[[Category: Theobald, D L.]]	+	[[Category: Theobald, D L]]
	[[Category: Dna binding protein-dna complex]]		[[Category: Dna binding protein-dna complex]]
	[[Category: Noncognate]]		[[Category: Noncognate]]

OCA at 11:25, 3 October 2014

OCA — Fri, 03 Oct 2014 11:25:10 GMT

←Older revision		Revision as of 11:25, 3 October 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_1pa6\| PDB=1pa6 \| SCENE= }}~~	+	==Crystal structure of the OXYTRICHA nova telomere end-binding protein complexed with noncognate ssDNA GGGGTTTTGAGG==
-	===Crystal structure of the OXYTRICHA nova telomere end-binding protein complexed with noncognate ssDNA GGGGTTTTGAGG===	+	<StructureSection load='1pa6' size='340' side='right' caption='[[1pa6]], [[Resolution\|resolution]] 2.45Å' scene=''>
-	~~{{ABSTRACT_PUBMED_12912928}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1pa6]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Sterkiella_nova Sterkiella nova]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PA6 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PA6 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1otc\|1otc]], [[1jb7\|1jb7]], [[1kix\|1kix]], [[1k8g\|1k8g]], [[1ph1\|1ph1]], [[1ph2\|1ph2]], [[1ph3\|1ph3]], [[1ph4\|1ph4]], [[1ph5\|1ph5]], [[1ph6\|1ph6]], [[1ph7\|1ph7]], [[1ph8\|1ph8]], [[1ph9\|1ph9]], [[1phj\|1phj]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">MAC-56A AND MAC-56K AND MAC-56S ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=200597 Sterkiella nova]), MAC-41A AND MAC-41S ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=200597 Sterkiella nova])</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=1pa6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pa6 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1pa6 RCSB], [http://www.ebi.ac.uk/pdbsum/1pa6 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/pa/1pa6_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 ==
		+	Sequence-specific protein recognition of single-stranded nucleic acids is critical for many fundamental cellular processes, such as DNA replication, DNA repair, transcription, translation, recombination, apoptosis and telomere maintenance. To explore the mechanisms of sequence-specific ssDNA recognition, we determined the crystal structures of 10 different non-cognate ssDNAs complexed with the Oxytricha nova telomere end-binding protein (OnTEBP) and evaluated their corresponding binding affinities (PDB ID codes 1PH1-1PH9 and 1PHJ). The thermodynamic and structural effects of these sequence perturbations could not have been predicted based solely upon the cognate structure. OnTEBP accommodates non-cognate nucleotides by both subtle adjustments and surprisingly large structural rearrangements in the ssDNA. In two complexes containing ssDNA intermediates that occur during telomere extension by telomerase, entire nucleotides are expelled from the complex. Concurrently, the sequence register of the ssDNA shifts to re-establish a more cognate-like pattern. This phenomenon, termed nucleotide shuffling, may be of general importance in protein recognition of single-stranded nucleic acids. This set of structural and thermodynamic data highlights a fundamental difference between protein recognition of ssDNA versus dsDNA.

-	~~==Function==~~	+	Nucleotide shuffling and ssDNA recognition in Oxytricha nova telomere end-binding protein complexes.,Theobald DL, Schultz SC EMBO J. 2003 Aug 15;22(16):4314-24. PMID:12912928<ref>PMID:12912928</ref>
-	~~[[http://www.uniprot.org/uniprot/TEBB_OXYNO TEBB_OXYNO]] May function as protective capping of the single-stranded telomeric overhang. May also participate~~ in telomere ~~length regulation during DNA replication~~. ~~Binds specifically to the T4G4~~-~~containing extension on the 3'strand and protects this region of the telomere from nuclease digestion and chemical modification~~. ~~[[http~~://www.uniprot.org/uniprot/TEBA_OXYNO TEBA_OXYNO]] May function as protective capping of the single-stranded telomeric overhang. May also participate in telomere length regulation during DNA replication. Binds specifically to the T4G4-containing extension on the 3'strand and protects this region of the telomere from nuclease digestion and chemical modification.	+

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[1pa6]] is~~ a ~~5 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Sterkiella_nova Sterkiella nova]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1PA6 OCA].~~	+	</div>
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:012912928</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Sterkiella nova]]		[[Category: Sterkiella nova]]
	[[Category: Schultz, S C.]]		[[Category: Schultz, S C.]]

OCA at 10:58, 16 April 2014

OCA — Wed, 16 Apr 2014 10:58:33 GMT

←Older revision		Revision as of 10:58, 16 April 2014
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-	[[Image:1pa6.png\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_1pa6", 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_1pa6\| PDB=1pa6 \| SCENE= }}		{{STRUCTURE_1pa6\| PDB=1pa6 \| SCENE= }}
-
	===Crystal structure of the OXYTRICHA nova telomere end-binding protein complexed with noncognate ssDNA GGGGTTTTGAGG===		===Crystal structure of the OXYTRICHA nova telomere end-binding protein complexed with noncognate ssDNA GGGGTTTTGAGG===
		+	{{ABSTRACT_PUBMED_12912928}}

-		+	==Function==
-	~~<!--~~	+	[[http://www.uniprot.org/uniprot/TEBB_OXYNO TEBB_OXYNO]] May function as protective capping of the single-stranded telomeric overhang. May also participate in telomere length regulation during DNA replication. Binds specifically to the T4G4-containing extension on the 3'strand and protects this region of the telomere from nuclease digestion and chemical modification. [[http://www.uniprot.org/uniprot/TEBA_OXYNO TEBA_OXYNO]] May function as protective capping of the single-stranded telomeric overhang. May also participate in telomere length regulation during DNA replication. Binds specifically to the T4G4-containing extension on the 3'strand and protects this region of the telomere from nuclease digestion and chemical modification.
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_12912928}}, adds~~ the ~~Publication Abstract~~ to the ~~page~~	+
-	~~(as it appears~~ on ~~PubMed at~~ http://www.~~pubmed~~.~~gov), where 12912928 is~~ the ~~PubMed ID number~~.	+
-	-->	+
-	~~{{ABSTRACT_PUBMED_12912928}}~~	+

	==About this Structure==		==About this Structure==
Line 22:		Line 10:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:012912928</ref><references group="xtra"/>	+	<ref group="xtra">PMID:012912928</ref><references group="xtra"/><references/>
	[[Category: Sterkiella nova]]		[[Category: Sterkiella nova]]
	[[Category: Schultz, S C.]]		[[Category: Schultz, S C.]]

OCA: Protected "1pa6" [edit=sysop:move=sysop]

OCA — Wed, 16 Nov 2011 11:21:49 GMT

Protected "1pa6" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:21, 16 November 2011

OCA at 11:21, 16 November 2011

OCA — Wed, 16 Nov 2011 11:21:48 GMT

←Older revision		Revision as of 11:21, 16 November 2011
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1pa6.png\|left\|200px]]		[[Image:1pa6.png\|left\|200px]]

Line 20:		Line 19:

	==About this Structure==		==About this Structure==
-	~~1PA6~~ is a 5 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Sterkiella_nova Sterkiella nova]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PA6 OCA].	+	[[1pa6]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Sterkiella_nova Sterkiella nova]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PA6 OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~12912928~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:012912928</ref><references group="xtra"/>
	[[Category: Sterkiella nova]]		[[Category: Sterkiella nova]]
	[[Category: Schultz, S C.]]		[[Category: Schultz, S C.]]
	[[Category: Theobald, D L.]]		[[Category: Theobald, D L.]]
		+	[[Category: Dna binding protein-dna complex]]
	[[Category: Noncognate]]		[[Category: Noncognate]]
	[[Category: Ob fold]]		[[Category: Ob fold]]
Line 35:		Line 35:
	[[Category: Single strand dna binding protein]]		[[Category: Single strand dna binding protein]]
	[[Category: Telomere]]		[[Category: Telomere]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 09:33:48 2009''

OCA at 07:33, 18 February 2009

OCA — Wed, 18 Feb 2009 07:33:50 GMT

←Older revision		Revision as of 07:33, 18 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	1PA6 is a ~~[[Protein complex]]~~ structure of sequences from [http://en.wikipedia.org/wiki/Sterkiella_nova Sterkiella nova]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PA6 OCA].	+	1PA6 is a 5 chains structure of sequences from [http://en.wikipedia.org/wiki/Sterkiella_nova Sterkiella nova]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PA6 OCA].

	==Reference==		==Reference==
-	~~Nucleotide shuffling and ssDNA recognition in Oxytricha nova telomere end-binding protein complexes., Theobald DL, Schultz SC, EMBO J. 2003 Aug 15;22(16):4314-24.~~ PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/12912928 12912928]~~	+	<ref group="xtra">PMID:12912928</ref><references group="xtra"/>
-	~~[[Category: Protein complex]]~~	+
	[[Category: Sterkiella nova]]		[[Category: Sterkiella nova]]
	[[Category: Schultz, S C.]]		[[Category: Schultz, S C.]]
Line 37:		Line 36:
	[[Category: Telomere]]		[[Category: Telomere]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Tue Jul 29 15~~:50:~~20 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 09:33:48 2009''