6qaj - Revision history

OCA at 11:56, 24 January 2024

2024-01-24T11:56:47Z

←Older revision		Revision as of 11:56, 24 January 2024
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	<StructureSection load='6qaj' size='340' side='right'caption='[[6qaj]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='6qaj' size='340' side='right'caption='[[6qaj]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6qaj]] is a 2 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=6QAJ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6QAJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6qaj]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_T4 Escherichia virus T4] and [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QAJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6QAJ 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='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.901Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~TRIM28, KAP1, RNF96, TIF1B ([http~~:/~~/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=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6qaj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qaj OCA], [~~http~~://pdbe.org/6qaj PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6qaj RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6qaj PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6qaj 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=6qaj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qaj OCA], [https://pdbe.org/6qaj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6qaj RCSB], [https://www.ebi.ac.uk/pdbsum/6qaj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6qaj ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/ENLYS_BPT4 ENLYS_BPT4]] Endolysin with lysozyme activity that degrades host peptidoglycans and participates with the holin and spanin proteins in the sequential events which lead to the programmed host cell lysis releasing the mature viral particles. Once the holin has permeabilized the host cell membrane, the endolysin can reach the periplasm and break down the peptidoglycan layer.<ref>PMID:22389108</ref>	+	[https://www.uniprot.org/uniprot/TIF1B_HUMAN TIF1B_HUMAN] Nuclear corepressor for KRAB domain-containing zinc finger proteins (KRAB-ZFPs). Mediates gene silencing by recruiting CHD3, a subunit of the nucleosome remodeling and deacetylation (NuRD) complex, and SETDB1 (which specifically methylates histone H3 at 'Lys-9' (H3K9me)) to the promoter regions of KRAB target genes. Enhances transcriptional repression by coordinating the increase in H3K9me, the decrease in histone H3 'Lys-9 and 'Lys-14' acetylation (H3K9ac and H3K14ac, respectively) and the disposition of HP1 proteins to silence gene expression. Recruitment of SETDB1 induces heterochromatinization. May play a role as a coactivator for CEBPB and NR3C1 in the transcriptional activation of ORM1. Also corepressor for ERBB4. Inhibits E2F1 activity by stimulating E2F1-HDAC1 complex formation and inhibiting E2F1 acetylation. May serve as a partial backup to prevent E2F1-mediated apoptosis in the absence of RB1. Important regulator of CDKN1A/p21(CIP1). Has E3 SUMO-protein ligase activity toward itself via its PHD-type zinc finger. Also specifically sumoylates IRF7, thereby inhibiting its transactivation activity. Ubiquitinates p53/TP53 leading to its proteosomal degradation; the function is enhanced by MAGEC2 and MAGEA2, and possibly MAGEA3 and MAGEA6.<ref>PMID:8769649</ref> <ref>PMID:9016654</ref> <ref>PMID:10347202</ref> <ref>PMID:11959841</ref> <ref>PMID:15882967</ref> <ref>PMID:16107876</ref> <ref>PMID:17178852</ref> <ref>PMID:16862143</ref> <ref>PMID:17079232</ref> <ref>PMID:17704056</ref> <ref>PMID:17942393</ref> <ref>PMID:18082607</ref> <ref>PMID:18060868</ref> <ref>PMID:20858735</ref> <ref>PMID:20864041</ref> <ref>PMID:20424263</ref> <ref>PMID:21940674</ref> [https://www.uniprot.org/uniprot/ENLYS_BPT4 ENLYS_BPT4] Endolysin with lysozyme activity that degrades host peptidoglycans and participates with the holin and spanin proteins in the sequential events which lead to the programmed host cell lysis releasing the mature viral particles. Once the holin has permeabilized the host cell membrane, the endolysin can reach the periplasm and break down the peptidoglycan layer.<ref>PMID:22389108</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Escherichia virus T4]]
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Modis, Y]]	+	[[Category: Modis Y]]
-	[[Category: Oda, S]]	+	[[Category: Oda S]]
-	[[Category: Stoll~~, G A~~]]	+	[[Category: Stoll GA]]
-	[[Category: Yu, M]]	+	[[Category: Yu M]]
-	~~[[Category: E3 ligase]]~~	+
-	~~[[Category: Endogenous retrovirus]]~~	+
-	~~[[Category: Epigenetic silencing]]~~	+
-	~~[[Category: Nuclear protein]]~~	+
-	~~[[Category: Retrotransposon]]~~	+
-	~~[[Category: Sumo]]~~	+
-	~~[[Category: Transcriptional repressor]]~~	+
-	~~[[Category: Transposable element]]~~	+
-	~~[[Category: Ubiquitin~~]]	+

OCA at 07:03, 31 July 2019

2019-07-31T07:03:19Z

←Older revision		Revision as of 07:03, 31 July 2019
Line 3:		Line 3:
	<StructureSection load='6qaj' size='340' side='right'caption='[[6qaj]], [[Resolution\|resolution]] 2.90Å' scene=''>		<StructureSection load='6qaj' size='340' side='right'caption='[[6qaj]], [[Resolution\|resolution]] 2.90Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6qaj]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QAJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6QAJ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6qaj]] is a 2 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=6QAJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6QAJ 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='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">TRIM28, KAP1, RNF96, TIF1B ([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=6qaj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qaj OCA], [http://pdbe.org/6qaj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6qaj RCSB], [http://www.ebi.ac.uk/pdbsum/6qaj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6qaj ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6qaj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qaj OCA], [http://pdbe.org/6qaj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6qaj RCSB], [http://www.ebi.ac.uk/pdbsum/6qaj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6qaj ProSAT]</span></td></tr>
	</table>		</table>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Modis, Y]]		[[Category: Modis, Y]]

OCA at 06:27, 24 July 2019

2019-07-24T06:27:25Z

←Older revision		Revision as of 06:27, 24 July 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6qaj is ~~ON HOLD~~ ~~until Paper~~ Publication	+	==Structure of the tripartite motif of KAP1/TRIM28==
		+	<StructureSection load='6qaj' size='340' side='right'caption='[[6qaj]], [[Resolution\|resolution]] 2.90Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6qaj]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QAJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6QAJ 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>
		+	<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=6qaj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qaj OCA], [http://pdbe.org/6qaj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6qaj RCSB], [http://www.ebi.ac.uk/pdbsum/6qaj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6qaj ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/ENLYS_BPT4 ENLYS_BPT4]] Endolysin with lysozyme activity that degrades host peptidoglycans and participates with the holin and spanin proteins in the sequential events which lead to the programmed host cell lysis releasing the mature viral particles. Once the holin has permeabilized the host cell membrane, the endolysin can reach the periplasm and break down the peptidoglycan layer.<ref>PMID:22389108</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Transcription of transposable elements is tightly regulated to prevent genome damage. KRAB domain-containing zinc finger proteins (KRAB-ZFPs) and KRAB-associated protein 1 (KAP1/TRIM28) play a key role in regulating retrotransposons. KRAB-ZFPs recognize specific retrotransposon sequences and recruit KAP1, inducing the assembly of an epigenetic silencing complex, with chromatin remodeling activities that repress transcription of the targeted retrotransposon and adjacent genes. Our biophysical and structural data show that the tripartite motif (TRIM) of KAP1 forms antiparallel dimers, which further assemble into tetramers and higher-order oligomers in a concentration-dependent manner. Structure-based mutations in the B-box 1 domain prevent higher-order oligomerization without significant loss of retrotransposon silencing activity, indicating that, in contrast to other TRIM-family proteins, self-assembly is not essential for KAP1 function. The crystal structure of the KAP1 TRIM dimer identifies the KRAB domain binding site in the coiled-coil domain near the dyad. Mutations at this site abolished KRAB binding and transcriptional silencing activity of KAP1. This work identifies the interaction interfaces in the KAP1 TRIM responsible for self-association and KRAB binding and establishes their role in retrotransposon silencing.

-	~~Authors: Stoll, G.A~~., Oda, S., Yu, M., ~~Modis~~, Y.	+	Structure of KAP1 tripartite motif identifies molecular interfaces required for retroelement silencing.,Stoll GA, Oda SI, Chong ZS, Yu M, McLaughlin SH, Modis Y Proc Natl Acad Sci U S A. 2019 Jul 9. pii: 1901318116. doi:, 10.1073/pnas.1901318116. PMID:31289231<ref>PMID:31289231</ref>

-	~~Description: Structure~~ of the ~~tripartite motif~~ of ~~KAP1~~/~~TRIM28~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category~~: ~~Unreleased Structures]]~~	+	</div>
-	~~[[Category: Yu, M]]~~	+	<div class="pdbe-citations 6qaj" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Oda, S~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Modis, Y]]		[[Category: Modis, Y]]
-	[[Category: Stoll, G.A]]	+	[[Category: Oda, S]]
		+	[[Category: Stoll, G A]]
		+	[[Category: Yu, M]]
		+	[[Category: E3 ligase]]
		+	[[Category: Endogenous retrovirus]]
		+	[[Category: Epigenetic silencing]]
		+	[[Category: Nuclear protein]]
		+	[[Category: Retrotransposon]]
		+	[[Category: Sumo]]
		+	[[Category: Transcriptional repressor]]
		+	[[Category: Transposable element]]
		+	[[Category: Ubiquitin]]

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

2018-12-26T07:03:03Z

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

←Older revision

Revision as of 07:03, 26 December 2018

OCA: New page: '''Unreleased structure''' The entry 6qaj is ON HOLD until Paper Publication Authors: Stoll, G.A., Oda, S., Yu, M., Modis, Y. Description: Structure of the tripartite motif of KAP1/TRI...

2018-12-26T07:03:02Z

New page: '''Unreleased structure''' The entry 6qaj is ON HOLD until Paper Publication Authors: Stoll, G.A., Oda, S., Yu, M., Modis, Y. Description: Structure of the tripartite motif of KAP1/TRI...

New page

'''Unreleased structure'''

The entry 6qaj is ON HOLD until Paper Publication

Authors: Stoll, G.A., Oda, S., Yu, M., Modis, Y.

Description: Structure of the tripartite motif of KAP1/TRIM28
[[Category: Unreleased Structures]]
[[Category: Yu, M]]
[[Category: Oda, S]]
[[Category: Modis, Y]]
[[Category: Stoll, G.A]]