3k6g - Revision history

OCA at 08:45, 7 February 2024

OCA — Wed, 07 Feb 2024 08:45:01 GMT

←Older revision		Revision as of 08:45, 7 February 2024
Line 3:		Line 3:
	<StructureSection load='3k6g' size='340' side='right'caption='[[3k6g]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='3k6g' size='340' side='right'caption='[[3k6g]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3k6g]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3K6G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3K6G FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3k6g]] 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=3K6G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3K6G 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='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.95Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~TERF2IP, RAP1, PP8000 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=9606 HUMAN]), TERF2, TRBF2, TRF2 ([https~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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'>[https://proteopedia.org/fgij/fg.htm?mol=3k6g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3k6g OCA], [https://pdbe.org/3k6g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3k6g RCSB], [https://www.ebi.ac.uk/pdbsum/3k6g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3k6g 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=3k6g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3k6g OCA], [https://pdbe.org/3k6g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3k6g RCSB], [https://www.ebi.ac.uk/pdbsum/3k6g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3k6g ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/TE2IP_HUMAN TE2IP_HUMAN]] Acts both as a regulator of telomere function and as a transcription regulator. Involved in the regulation of telomere length and protection as a component of the shelterin complex (telosome). In contrast to other components of the shelterin complex, it is dispensible for telomere capping and does not participate in the protection of telomeres against non-homologous end-joining (NHEJ)-mediated repair. Instead, it is required to negatively regulate telomere recombination and is essential for repressing homology-directed repair (HDR), which can affect telomere length. Does not bind DNA directly: recruited to telomeric double-stranded 5'-TTAGGG-3' repeats via its interaction with TERF2. Independently of its function in telomeres, also acts as a transcription regulator: recruited to extratelomeric 5'-TTAGGG-3' sites via its association with TERF2 or other factors, and regulates gene expression. When cytoplasmic, associates with the I-kappa-B-kinase (IKK) complex and acts as a regulator of the NF-kappa-B signaling by promoting IKK-mediated phosphorylation of RELA/p65, leading to activate expression of NF-kappa-B target genes.<ref>PMID:16166375</ref> <ref>PMID:19763083</ref> [[https://www.uniprot.org/uniprot/TERF2_HUMAN TERF2_HUMAN]] Binds the telomeric double-stranded 5'-TTAGGG-3' repeat and plays a central role in telomere maintenance and protection against end-to-end fusion of chromosomes. In addition to its telomeric DNA-binding role, required to recruit a number of factors and enzymes required for telomere protection, including the shelterin complex, TERF2IP/RAP1 and DCLRE1B/Apollo. Component of the shelterin complex (telosome) that is involved in the regulation of telomere length and protection. Shelterin associates with arrays of double-stranded 5'-TTAGGG-3' repeats added by telomerase and protects chromosome ends; without its protective activity, telomeres are no longer hidden from the DNA damage surveillance and chromosome ends are inappropriately processed by DNA repair pathways. Together with DCLRE1B/Apollo, plays a key role in telomeric loop (T loop) formation by generating 3' single-stranded overhang at the leading end telomeres: T loops have been proposed to protect chromosome ends from degradation and repair. Required both to recruit DCLRE1B/Apollo to telomeres and activate the exonuclease activity of DCLRE1B/Apollo. Preferentially binds to positive supercoiled DNA. Together with DCLRE1B/Apollo, required to control the amount of DNA topoisomerase (TOP1, TOP2A and TOP2B) needed for telomere replication during fork passage and prevent aberrant telomere topology. Recruits TERF2IP/RAP1 to telomeres, thereby participating in to repressing homology-directed repair (HDR), which can affect telomere length.<ref>PMID:9476899</ref> <ref>PMID:16166375</ref> <ref>PMID:20655466</ref>	+	[https://www.uniprot.org/uniprot/TE2IP_HUMAN TE2IP_HUMAN] Acts both as a regulator of telomere function and as a transcription regulator. Involved in the regulation of telomere length and protection as a component of the shelterin complex (telosome). In contrast to other components of the shelterin complex, it is dispensible for telomere capping and does not participate in the protection of telomeres against non-homologous end-joining (NHEJ)-mediated repair. Instead, it is required to negatively regulate telomere recombination and is essential for repressing homology-directed repair (HDR), which can affect telomere length. Does not bind DNA directly: recruited to telomeric double-stranded 5'-TTAGGG-3' repeats via its interaction with TERF2. Independently of its function in telomeres, also acts as a transcription regulator: recruited to extratelomeric 5'-TTAGGG-3' sites via its association with TERF2 or other factors, and regulates gene expression. When cytoplasmic, associates with the I-kappa-B-kinase (IKK) complex and acts as a regulator of the NF-kappa-B signaling by promoting IKK-mediated phosphorylation of RELA/p65, leading to activate expression of NF-kappa-B target genes.<ref>PMID:16166375</ref> <ref>PMID:19763083</ref>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Repressor activator protein 1 (RAP1) is the most highly conserved telomere protein. It is involved in protecting chromosome ends in fission yeast and promoting gene silencing in Saccharomyces cerevisiae, whereas it represses homology-directed recombination at telomeres in mammals. To understand how RAP1 has such diverse functions at telomeres, we solved the crystal or solution structures of the RAP1 C-terminal (RCT) domains of RAP1 from multiple organisms in complex with their respective protein-binding partners. Our analysis establishes RAP1(RCT) as an evolutionarily conserved protein-protein interaction module. In mammalian and fission yeast cells, this module interacts with TRF2 and Taz1, respectively, targeting RAP1 to chromosome ends for telomere protection. In contrast, S. cerevisiae RAP1 uses its RCT domain to recruit Sir3 to telomeres to mediate gene silencing. Together, our results show that, depending on the organism, the evolutionarily conserved RAP1 RCT motif has diverse functional roles at telomeres.	+
-		+
-	A conserved motif within RAP1 has diversified roles in telomere protection and regulation in different organisms.,Chen Y, Rai R, Zhou ZR, Kanoh J, Ribeyre C, Yang Y, Zheng H, Damay P, Wang F, Tsujii H, Hiraoka Y, Shore D, Hu HY, Chang S, Lei M Nat Struct Mol Biol. 2011 Jan 9. PMID:21217703<ref>PMID:21217703</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 3k6g" style="background-color:#fffaf0;"></div~~>	+
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Chang, S]]	+	[[Category: Chang S]]
-	[[Category: Chen, Y]]	+	[[Category: Chen Y]]
-	[[Category: Lei, M]]	+	[[Category: Lei M]]
-	[[Category: Rai, R]]	+	[[Category: Rai R]]
-	[[Category: Yang~~, Y T~~]]	+	[[Category: Yang YT]]
-	[[Category: Zheng, H]]	+	[[Category: Zheng H]]
-	~~[[Category: Cell cycle]]~~	+
-	~~[[Category: Chromosomal protein]]~~	+
-	~~[[Category: Dna-binding]]~~	+
-	~~[[Category: Helix]]~~	+
-	~~[[Category: Nucleus]]~~	+
-	~~[[Category: Phosphoprotein]]~~	+
-	~~[[Category: Protein binding]]~~	+
-	~~[[Category: Telomere~~]]	+

OCA at 13:33, 4 May 2022

OCA — Wed, 04 May 2022 13:33:39 GMT

←Older revision		Revision as of 13:33, 4 May 2022
Line 1:		Line 1:

	==Crystal structure of Rap1 and TRF2 complex==		==Crystal structure of Rap1 and TRF2 complex==
-	<StructureSection load='3k6g' size='340' side='right' caption='[[3k6g]], [[Resolution\|resolution]] 1.95Å' scene=''>	+	<StructureSection load='3k6g' size='340' side='right'caption='[[3k6g]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3k6g]] 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=3K6G OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3K6G FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3k6g]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3K6G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3K6G 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">TERF2IP, RAP1, PP8000 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), TERF2, TRBF2, TRF2 ([~~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">TERF2IP, RAP1, PP8000 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), TERF2, TRBF2, TRF2 ([https://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=3k6g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3k6g OCA], [~~http~~://pdbe.org/3k6g PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3k6g RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3k6g PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3k6g 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=3k6g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3k6g OCA], [https://pdbe.org/3k6g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3k6g RCSB], [https://www.ebi.ac.uk/pdbsum/3k6g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3k6g ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/TE2IP_HUMAN TE2IP_HUMAN]] Acts both as a regulator of telomere function and as a transcription regulator. Involved in the regulation of telomere length and protection as a component of the shelterin complex (telosome). In contrast to other components of the shelterin complex, it is dispensible for telomere capping and does not participate in the protection of telomeres against non-homologous end-joining (NHEJ)-mediated repair. Instead, it is required to negatively regulate telomere recombination and is essential for repressing homology-directed repair (HDR), which can affect telomere length. Does not bind DNA directly: recruited to telomeric double-stranded 5'-TTAGGG-3' repeats via its interaction with TERF2. Independently of its function in telomeres, also acts as a transcription regulator: recruited to extratelomeric 5'-TTAGGG-3' sites via its association with TERF2 or other factors, and regulates gene expression. When cytoplasmic, associates with the I-kappa-B-kinase (IKK) complex and acts as a regulator of the NF-kappa-B signaling by promoting IKK-mediated phosphorylation of RELA/p65, leading to activate expression of NF-kappa-B target genes.<ref>PMID:16166375</ref> <ref>PMID:19763083</ref> [[~~http~~://www.uniprot.org/uniprot/TERF2_HUMAN TERF2_HUMAN]] Binds the telomeric double-stranded 5'-TTAGGG-3' repeat and plays a central role in telomere maintenance and protection against end-to-end fusion of chromosomes. In addition to its telomeric DNA-binding role, required to recruit a number of factors and enzymes required for telomere protection, including the shelterin complex, TERF2IP/RAP1 and DCLRE1B/Apollo. Component of the shelterin complex (telosome) that is involved in the regulation of telomere length and protection. Shelterin associates with arrays of double-stranded 5'-TTAGGG-3' repeats added by telomerase and protects chromosome ends; without its protective activity, telomeres are no longer hidden from the DNA damage surveillance and chromosome ends are inappropriately processed by DNA repair pathways. Together with DCLRE1B/Apollo, plays a key role in telomeric loop (T loop) formation by generating 3' single-stranded overhang at the leading end telomeres: T loops have been proposed to protect chromosome ends from degradation and repair. Required both to recruit DCLRE1B/Apollo to telomeres and activate the exonuclease activity of DCLRE1B/Apollo. Preferentially binds to positive supercoiled DNA. Together with DCLRE1B/Apollo, required to control the amount of DNA topoisomerase (TOP1, TOP2A and TOP2B) needed for telomere replication during fork passage and prevent aberrant telomere topology. Recruits TERF2IP/RAP1 to telomeres, thereby participating in to repressing homology-directed repair (HDR), which can affect telomere length.<ref>PMID:9476899</ref> <ref>PMID:16166375</ref> <ref>PMID:20655466</ref>	+	[[https://www.uniprot.org/uniprot/TE2IP_HUMAN TE2IP_HUMAN]] Acts both as a regulator of telomere function and as a transcription regulator. Involved in the regulation of telomere length and protection as a component of the shelterin complex (telosome). In contrast to other components of the shelterin complex, it is dispensible for telomere capping and does not participate in the protection of telomeres against non-homologous end-joining (NHEJ)-mediated repair. Instead, it is required to negatively regulate telomere recombination and is essential for repressing homology-directed repair (HDR), which can affect telomere length. Does not bind DNA directly: recruited to telomeric double-stranded 5'-TTAGGG-3' repeats via its interaction with TERF2. Independently of its function in telomeres, also acts as a transcription regulator: recruited to extratelomeric 5'-TTAGGG-3' sites via its association with TERF2 or other factors, and regulates gene expression. When cytoplasmic, associates with the I-kappa-B-kinase (IKK) complex and acts as a regulator of the NF-kappa-B signaling by promoting IKK-mediated phosphorylation of RELA/p65, leading to activate expression of NF-kappa-B target genes.<ref>PMID:16166375</ref> <ref>PMID:19763083</ref> [[https://www.uniprot.org/uniprot/TERF2_HUMAN TERF2_HUMAN]] Binds the telomeric double-stranded 5'-TTAGGG-3' repeat and plays a central role in telomere maintenance and protection against end-to-end fusion of chromosomes. In addition to its telomeric DNA-binding role, required to recruit a number of factors and enzymes required for telomere protection, including the shelterin complex, TERF2IP/RAP1 and DCLRE1B/Apollo. Component of the shelterin complex (telosome) that is involved in the regulation of telomere length and protection. Shelterin associates with arrays of double-stranded 5'-TTAGGG-3' repeats added by telomerase and protects chromosome ends; without its protective activity, telomeres are no longer hidden from the DNA damage surveillance and chromosome ends are inappropriately processed by DNA repair pathways. Together with DCLRE1B/Apollo, plays a key role in telomeric loop (T loop) formation by generating 3' single-stranded overhang at the leading end telomeres: T loops have been proposed to protect chromosome ends from degradation and repair. Required both to recruit DCLRE1B/Apollo to telomeres and activate the exonuclease activity of DCLRE1B/Apollo. Preferentially binds to positive supercoiled DNA. Together with DCLRE1B/Apollo, required to control the amount of DNA topoisomerase (TOP1, TOP2A and TOP2B) needed for telomere replication during fork passage and prevent aberrant telomere topology. Recruits TERF2IP/RAP1 to telomeres, thereby participating in to repressing homology-directed repair (HDR), which can affect telomere length.<ref>PMID:9476899</ref> <ref>PMID:16166375</ref> <ref>PMID:20655466</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 24:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Chang, S]]		[[Category: Chang, S]]
	[[Category: Chen, Y]]		[[Category: Chen, Y]]

OCA at 17:42, 5 August 2016

OCA — Fri, 05 Aug 2016 17:42:19 GMT

←Older revision		Revision as of 17:42, 5 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of Rap1 and TRF2 complex==		==Crystal structure of Rap1 and TRF2 complex==
	<StructureSection load='3k6g' size='340' side='right' caption='[[3k6g]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='3k6g' size='340' side='right' caption='[[3k6g]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3k6g]] 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=3K6G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3K6G FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3k6g]] 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=3K6G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3K6G 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">TERF2IP, RAP1, PP8000 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 ~~Homo sapiens~~]), TERF2, TRBF2, TRF2 ([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">TERF2IP, RAP1, PP8000 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN]), TERF2, TRBF2, TRF2 ([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=3k6g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3k6g OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3k6g RCSB], [http://www.ebi.ac.uk/pdbsum/3k6g 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=3k6g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3k6g OCA], [http://pdbe.org/3k6g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3k6g RCSB], [http://www.ebi.ac.uk/pdbsum/3k6g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3k6g ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 17:		Line 18:
	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 3k6g" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Chang, S]]		[[Category: Chang, S]]
	[[Category: Chen, Y]]		[[Category: Chen, Y]]

OCA at 20:43, 25 December 2014

OCA — Thu, 25 Dec 2014 20:43:20 GMT

←Older revision		Revision as of 20:43, 25 December 2014
Line 7:		Line 7:
	<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=3k6g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3k6g OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3k6g RCSB], [http://www.ebi.ac.uk/pdbsum/3k6g 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=3k6g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3k6g OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3k6g RCSB], [http://www.ebi.ac.uk/pdbsum/3k6g PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/TE2IP_HUMAN TE2IP_HUMAN]] Acts both as a regulator of telomere function and as a transcription regulator. Involved in the regulation of telomere length and protection as a component of the shelterin complex (telosome). In contrast to other components of the shelterin complex, it is dispensible for telomere capping and does not participate in the protection of telomeres against non-homologous end-joining (NHEJ)-mediated repair. Instead, it is required to negatively regulate telomere recombination and is essential for repressing homology-directed repair (HDR), which can affect telomere length. Does not bind DNA directly: recruited to telomeric double-stranded 5'-TTAGGG-3' repeats via its interaction with TERF2. Independently of its function in telomeres, also acts as a transcription regulator: recruited to extratelomeric 5'-TTAGGG-3' sites via its association with TERF2 or other factors, and regulates gene expression. When cytoplasmic, associates with the I-kappa-B-kinase (IKK) complex and acts as a regulator of the NF-kappa-B signaling by promoting IKK-mediated phosphorylation of RELA/p65, leading to activate expression of NF-kappa-B target genes.<ref>PMID:16166375</ref> <ref>PMID:19763083</ref> [[http://www.uniprot.org/uniprot/TERF2_HUMAN TERF2_HUMAN]] Binds the telomeric double-stranded 5'-TTAGGG-3' repeat and plays a central role in telomere maintenance and protection against end-to-end fusion of chromosomes. In addition to its telomeric DNA-binding role, required to recruit a number of factors and enzymes required for telomere protection, including the shelterin complex, TERF2IP/RAP1 and DCLRE1B/Apollo. Component of the shelterin complex (telosome) that is involved in the regulation of telomere length and protection. Shelterin associates with arrays of double-stranded 5'-TTAGGG-3' repeats added by telomerase and protects chromosome ends; without its protective activity, telomeres are no longer hidden from the DNA damage surveillance and chromosome ends are inappropriately processed by DNA repair pathways. Together with DCLRE1B/Apollo, plays a key role in telomeric loop (T loop) formation by generating 3' single-stranded overhang at the leading end telomeres: T loops have been proposed to protect chromosome ends from degradation and repair. Required both to recruit DCLRE1B/Apollo to telomeres and activate the exonuclease activity of DCLRE1B/Apollo. Preferentially binds to positive supercoiled DNA. Together with DCLRE1B/Apollo, required to control the amount of DNA topoisomerase (TOP1, TOP2A and TOP2B) needed for telomere replication during fork passage and prevent aberrant telomere topology. Recruits TERF2IP/RAP1 to telomeres, thereby participating in to repressing homology-directed repair (HDR), which can affect telomere length.<ref>PMID:9476899</ref> <ref>PMID:16166375</ref> <ref>PMID:20655466</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==

OCA at 17:47, 18 December 2014

OCA — Thu, 18 Dec 2014 17:47:33 GMT

←Older revision		Revision as of 17:47, 18 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3k6g\| PDB~~=3k6g \| ~~SCENE~~= }}	+	==Crystal structure of Rap1 and TRF2 complex==
-	===~~Crystal~~ structure ~~of Rap1 and~~ TRF2 ~~complex~~===	+	<StructureSection load='3k6g' size='340' side='right' caption='[[3k6g]], [[Resolution\|resolution]] 1.95Å' scene=''>
-	~~{{ABSTRACT_PUBMED_21217703}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3k6g]] 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=3K6G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3K6G 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>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TERF2IP, RAP1, PP8000 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens]), TERF2, TRBF2, TRF2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 Homo sapiens])</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=3k6g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3k6g OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3k6g RCSB], [http://www.ebi.ac.uk/pdbsum/3k6g PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Repressor activator protein 1 (RAP1) is the most highly conserved telomere protein. It is involved in protecting chromosome ends in fission yeast and promoting gene silencing in Saccharomyces cerevisiae, whereas it represses homology-directed recombination at telomeres in mammals. To understand how RAP1 has such diverse functions at telomeres, we solved the crystal or solution structures of the RAP1 C-terminal (RCT) domains of RAP1 from multiple organisms in complex with their respective protein-binding partners. Our analysis establishes RAP1(RCT) as an evolutionarily conserved protein-protein interaction module. In mammalian and fission yeast cells, this module interacts with TRF2 and Taz1, respectively, targeting RAP1 to chromosome ends for telomere protection. In contrast, S. cerevisiae RAP1 uses its RCT domain to recruit Sir3 to telomeres to mediate gene silencing. Together, our results show that, depending on the organism, the evolutionarily conserved RAP1 RCT motif has diverse functional roles at telomeres.

-	~~==Function==~~	+	A conserved motif within RAP1 has diversified roles in telomere protection and regulation in different organisms.,Chen Y, Rai R, Zhou ZR, Kanoh J, Ribeyre C, Yang Y, Zheng H, Damay P, Wang F, Tsujii H, Hiraoka Y, Shore D, Hu HY, Chang S, Lei M Nat Struct Mol Biol. 2011 Jan 9. PMID:21217703<ref>PMID:21217703</ref>
-	~~[[http://www.uniprot.org/uniprot/TE2IP_HUMAN TE2IP_HUMAN]] Acts both as a regulator of telomere function and as a transcription regulator. Involved~~ in ~~the regulation of~~ telomere ~~length and~~ protection ~~as a component of the shelterin complex (telosome). In contrast to other components of the shelterin complex, it is dispensible for telomere capping~~ and ~~does not participate~~ in ~~the protection of telomeres against non-homologous end-joining (NHEJ)-mediated repair~~. ~~Instead~~, ~~it is required to negatively regulate telomere recombination and is essential for repressing homology-directed repair (HDR)~~, ~~which can affect telomere length. Does not bind DNA directly: recruited to telomeric double-stranded 5'-TTAGGG-3' repeats via its interaction with TERF2. Independently of its function in telomeres~~, ~~also acts as a transcription regulator: recruited to extratelomeric 5'-TTAGGG-3' sites via its association with TERF2 or other factors~~, ~~and regulates gene expression. When cytoplasmic~~, ~~associates with the I-kappa-B-kinase (IKK) complex and acts as a regulator of the NF-kappa-B signaling by promoting IKK-mediated phosphorylation of RELA/p65~~, leading to activate expression of NF-kappa-B target genes.<ref>PMID:16166375</ref> <ref>PMID:19763083</ref> [[http://www.uniprot.org/uniprot/TERF2_HUMAN TERF2_HUMAN]] Binds the telomeric double-stranded 5'-TTAGGG-3' repeat and plays a central role in telomere maintenance and protection against end-to-end fusion of chromosomes. In addition to its telomeric DNA-binding role, ~~required to recruit a number of factors and enzymes required for telomere protection~~, ~~including the shelterin complex~~, TERF2IP/RAP1 and DCLRE1B/Apollo. Component of the shelterin complex (telosome) that is involved in the regulation of telomere length and protection. Shelterin associates with arrays of double-stranded 5'-TTAGGG-3' repeats added by telomerase and protects chromosome ends; without its protective activity, ~~telomeres are no longer hidden from the DNA damage surveillance and chromosome ends are inappropriately processed by DNA repair pathways. Together with DCLRE1B/Apollo~~, plays a key role in telomeric loop (T loop) formation by generating 3' single-stranded overhang at the leading end telomeres: T loops have been proposed to protect chromosome ends from degradation and repair. Required both to recruit DCLRE1B/Apollo to telomeres and activate the exonuclease activity of DCLRE1B/Apollo. Preferentially binds to positive supercoiled DNA. Together with DCLRE1B/Apollo, ~~required to control the amount of DNA topoisomerase (TOP1~~, ~~TOP2A and TOP2B) needed for telomere replication during fork passage and prevent aberrant telomere topology. Recruits TERF2IP/RAP1 to telomeres~~, ~~thereby participating in to repressing homology-directed repair (HDR)~~, ~~which can affect telomere length~~.~~<ref>~~PMID:~~9476899</ref> <ref>PMID:16166375</ref>~~ <ref>PMID:~~20655466~~</ref>	+

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[3k6g]] 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=3K6G OCA].~~	+	</div>
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:021217703</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Chang, S.]]	+	[[Category: Chang, S]]
-	[[Category: Chen, Y.]]	+	[[Category: Chen, Y]]
-	[[Category: Lei, M.]]	+	[[Category: Lei, M]]
-	[[Category: Rai, R.]]	+	[[Category: Rai, R]]
-	[[Category: Yang, Y T.]]	+	[[Category: Yang, Y T]]
-	[[Category: Zheng, H.]]	+	[[Category: Zheng, H]]
	[[Category: Cell cycle]]		[[Category: Cell cycle]]
	[[Category: Chromosomal protein]]		[[Category: Chromosomal protein]]

OCA at 02:18, 4 April 2013

OCA — Thu, 04 Apr 2013 02:18:00 GMT

←Older revision		Revision as of 02:18, 4 April 2013
Line 1:		Line 1:
-	[[Image:3k6g.png\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_3k6g", 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_3k6g\| PDB=3k6g \| SCENE= }}		{{STRUCTURE_3k6g\| PDB=3k6g \| SCENE= }}
-
	===Crystal structure of Rap1 and TRF2 complex===		===Crystal structure of Rap1 and TRF2 complex===
		+	{{ABSTRACT_PUBMED_21217703}}

-		+	==Function==
-	<!--	+	[[http://www.uniprot.org/uniprot/TE2IP_HUMAN TE2IP_HUMAN]] Acts both as a regulator of telomere function and as a transcription regulator. Involved in the regulation of telomere length and protection as a component of the shelterin complex (telosome). In contrast to other components of the shelterin complex, it is dispensible for telomere capping and does not participate in the protection of telomeres against non-homologous end-joining (NHEJ)-mediated repair. Instead, it is required to negatively regulate telomere recombination and is essential for repressing homology-directed repair (HDR), which can affect telomere length. Does not bind DNA directly: recruited to telomeric double-stranded 5'-TTAGGG-3' repeats via its interaction with TERF2. Independently of its function in telomeres, also acts as a transcription regulator: recruited to extratelomeric 5'-TTAGGG-3' sites via its association with TERF2 or other factors, and regulates gene expression. When cytoplasmic, associates with the I-kappa-B-kinase (IKK) complex and acts as a regulator of the NF-kappa-B signaling by promoting IKK-mediated phosphorylation of RELA/p65, leading to activate expression of NF-kappa-B target genes.<ref>PMID:16166375</ref> <ref>PMID:19763083</ref> [[http://www.uniprot.org/uniprot/TERF2_HUMAN TERF2_HUMAN]] Binds the telomeric double-stranded 5'-TTAGGG-3' repeat and plays a central role in telomere maintenance and protection against end-to-end fusion of chromosomes. In addition to its telomeric DNA-binding role, required to recruit a number of factors and enzymes required for telomere protection, including the shelterin complex, TERF2IP/RAP1 and DCLRE1B/Apollo. Component of the shelterin complex (telosome) that is involved in the regulation of telomere length and protection. Shelterin associates with arrays of double-stranded 5'-TTAGGG-3' repeats added by telomerase and protects chromosome ends; without its protective activity, telomeres are no longer hidden from the DNA damage surveillance and chromosome ends are inappropriately processed by DNA repair pathways. Together with DCLRE1B/Apollo, plays a key role in telomeric loop (T loop) formation by generating 3' single-stranded overhang at the leading end telomeres: T loops have been proposed to protect chromosome ends from degradation and repair. Required both to recruit DCLRE1B/Apollo to telomeres and activate the exonuclease activity of DCLRE1B/Apollo. Preferentially binds to positive supercoiled DNA. Together with DCLRE1B/Apollo, required to control the amount of DNA topoisomerase (TOP1, TOP2A and TOP2B) needed for telomere replication during fork passage and prevent aberrant telomere topology. Recruits TERF2IP/RAP1 to telomeres, thereby participating in to repressing homology-directed repair (HDR), which can affect telomere length.<ref>PMID:9476899</ref> <ref>PMID:16166375</ref> <ref>PMID:20655466</ref>
-	~~The line below this paragraph~~, ~~{{ABSTRACT_PUBMED_21217703}}~~, ~~adds the Publication Abstract~~ to the ~~page~~	+
-	(as ~~it appears on PubMed at~~ http://www.~~pubmed~~.~~gov)~~, ~~where 21217703~~ is the ~~PubMed ID number~~.	+
-	-->	+
-	~~{{ABSTRACT_PUBMED_21217703}}~~	+

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

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~21217703~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:021217703</ref><references group="xtra"/><references/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Chang, S.]]		[[Category: Chang, S.]]
Line 30:		Line 18:
	[[Category: Yang, Y T.]]		[[Category: Yang, Y T.]]
	[[Category: Zheng, H.]]		[[Category: Zheng, H.]]
		+	[[Category: Cell cycle]]
		+	[[Category: Chromosomal protein]]
		+	[[Category: Dna-binding]]
		+	[[Category: Helix]]
		+	[[Category: Nucleus]]
		+	[[Category: Phosphoprotein]]
		+	[[Category: Protein binding]]
		+	[[Category: Telomere]]

OCA at 12:25, 26 January 2011

OCA — Wed, 26 Jan 2011 12:25:16 GMT

←Older revision		Revision as of 12:25, 26 January 2011
Line 11:		Line 11:
	===Crystal structure of Rap1 and TRF2 complex===		===Crystal structure of Rap1 and TRF2 complex===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_21217703}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 21217703 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_21217703}}

	==About this Structure==		==About this Structure==
	[[3k6g]] 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=3K6G OCA].		[[3k6g]] 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=3K6G OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:21217703</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Chang, S.]]		[[Category: Chang, S.]]

OCA: Protected "3k6g" [edit=sysop:move=sysop]

OCA — Wed, 12 Jan 2011 05:24:34 GMT

Protected "3k6g" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:24, 12 January 2011

OCA at 05:24, 12 January 2011

OCA — Wed, 12 Jan 2011 05:24:30 GMT

←Older revision		Revision as of 05:24, 12 January 2011
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-	~~{{Seed}}~~	+	[[Image:3k6g.png\|left\|200px]]
-	[[Image:3k6g.~~jpg~~\|left\|200px]]	+

	<!--		<!--
Line 14:		Line 13:

	==About this Structure==		==About this Structure==
-	~~3K6G~~ is a 6 ~~chains~~ structure with ~~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=3K6G OCA].	+	[[3k6g]] 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=3K6G OCA].
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Chang, S.]]		[[Category: Chang, S.]]
Line 22:		Line 21:
	[[Category: Yang, Y T.]]		[[Category: Yang, Y T.]]
	[[Category: Zheng, H.]]		[[Category: Zheng, H.]]
-	[[Category: Cell cycle]]
-	[[Category: Chromosomal protein]]
-	[[Category: Dna-binding]]
-	[[Category: Helix]]
-	[[Category: Nucleus]]
-	[[Category: Phosphoprotein]]
-	[[Category: Protein binding]]
-	[[Category: Telomere]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Oct 13 10:47:01 2010''

OCA at 07:37, 13 October 2010

OCA — Wed, 13 Oct 2010 07:37:13 GMT

←Older revision		Revision as of 07:37, 13 October 2010
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:3k6g.jpg\|left\|200px]]

-	The ~~entry 3k6g~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3k6g", 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_3k6g\| PDB=3k6g \| SCENE= }}

-	~~Authors: Chen, Y., Rai, R., Yang, Y.T., Zheng, H., Chang, S., Lei, M.~~	+	===Crystal structure of Rap1 and TRF2 complex===

-	Description: Crystal structure of Rap1 and TRF2 complex

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Oct ~~28 12:57~~:47 ~~2009~~''	+	==About this Structure==
		+	3K6G is a 6 chains structure with 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=3K6G OCA].
		+	[[Category: Homo sapiens]]
		+	[[Category: Chang, S.]]
		+	[[Category: Chen, Y.]]
		+	[[Category: Lei, M.]]
		+	[[Category: Rai, R.]]
		+	[[Category: Yang, Y T.]]
		+	[[Category: Zheng, H.]]
		+	[[Category: Cell cycle]]
		+	[[Category: Chromosomal protein]]
		+	[[Category: Dna-binding]]
		+	[[Category: Helix]]
		+	[[Category: Nucleus]]
		+	[[Category: Phosphoprotein]]
		+	[[Category: Protein binding]]
		+	[[Category: Telomere]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Oct 13 10:47:01 2010''