5h7g - Revision history

OCA at 07:26, 9 August 2023

OCA — Wed, 09 Aug 2023 07:26:16 GMT

←Older revision		Revision as of 07:26, 9 August 2023
Line 3:		Line 3:
	<StructureSection load='5h7g' size='340' side='right'caption='[[5h7g]], [[Resolution\|resolution]] 1.85Å' scene=''>		<StructureSection load='5h7g' size='340' side='right'caption='[[5h7g]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5h7g]] is a 4 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=5H7G OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5H7G FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5h7g]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_phage_T7 Escherichia phage T7] 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=5H7G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5H7G FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.85Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~>[[5h7h\|5h7h]]</td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~"><~~b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">BCL6, BCL5, LAZ3, ZBTB27, ZNF51 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])~~</td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5h7g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h7g OCA], [https://pdbe.org/5h7g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5h7g RCSB], [https://www.ebi.ac.uk/pdbsum/5h7g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5h7g 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=5h7g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h7g OCA], [~~http~~://pdbe.org/5h7g PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5h7g RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5h7g PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5h7g ProSAT]</span></td></tr>	+
	</table>		</table>
	== Disease ==		== Disease ==
-	[~~[http~~://www.uniprot.org/uniprot/BCL6_HUMAN BCL6_HUMAN]] Note=Chromosomal aberrations involving BCL6 may be a cause of B-cell non-Hodgkin lymphoma. Translocation t(3;14)(q27;q32); translocation t(3;22)(q27;q11) with immunoglobulin gene regions. Note=A chromosomal aberration involving BCL6 may be a cause of a form of B-cell leukemia. Translocation t(3;11)(q27;q23) with POU2AF1/OBF1. Note=A chromosomal aberration involving BCL6 may be a cause of lymphoma. Translocation t(3;4)(q27;p11) with ARHH/TTF.	+	[https://www.uniprot.org/uniprot/BCL6_HUMAN BCL6_HUMAN] Note=Chromosomal aberrations involving BCL6 may be a cause of B-cell non-Hodgkin lymphoma. Translocation t(3;14)(q27;q32); translocation t(3;22)(q27;q11) with immunoglobulin gene regions. Note=A chromosomal aberration involving BCL6 may be a cause of a form of B-cell leukemia. Translocation t(3;11)(q27;q23) with POU2AF1/OBF1. Note=A chromosomal aberration involving BCL6 may be a cause of lymphoma. Translocation t(3;4)(q27;p11) with ARHH/TTF.
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/BCL6_HUMAN BCL6_HUMAN]] Transcriptional repressor which is required for germinal center formation and antibody affinity maturation. Probably plays an important role in lymphomagenesis.<ref>PMID:9649500</ref> <ref>PMID:18280243</ref>	+	[https://www.uniprot.org/uniprot/BCL6_HUMAN BCL6_HUMAN] Transcriptional repressor which is required for germinal center formation and antibody affinity maturation. Probably plays an important role in lymphomagenesis.<ref>PMID:9649500</ref> <ref>PMID:18280243</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 29:		Line 28:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Escherichia phage T7]]
		+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Ida, K]]	+	[[Category: Ida K]]
-	[[Category: Lane, W]]	+	[[Category: Lane W]]
-	[[Category: Snell, G]]	+	[[Category: Snell G]]
-	[[Category: Sogabe, S]]	+	[[Category: Sogabe S]]
-	~~[[Category: Complex]]~~	+
-	~~[[Category: Inhibitor]]~~	+
-	~~[[Category: Transcription repressor]]~~	+
-	~~[[Category: Transcription-inhibitor complex~~]]	+

OCA at 06:54, 20 May 2020

OCA — Wed, 20 May 2020 06:54:32 GMT

←Older revision		Revision as of 06:54, 20 May 2020
Line 1:		Line 1:

	==Crystal structure of the BCL6 BTB domain in complex with F1324==		==Crystal structure of the BCL6 BTB domain in complex with F1324==
-	<StructureSection load='5h7g' size='340' side='right' caption='[[5h7g]], [[Resolution\|resolution]] 1.85Å' scene=''>	+	<StructureSection load='5h7g' size='340' side='right'caption='[[5h7g]], [[Resolution\|resolution]] 1.85Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5h7g]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5H7G OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5H7G FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5h7g]] is a 4 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=5H7G OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5H7G FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5h7h\|5h7h]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5h7h\|5h7h]]</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=5h7g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h7g OCA], [http://pdbe.org/5h7g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5h7g RCSB], [http://www.ebi.ac.uk/pdbsum/5h7g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5h7g ProSAT]</span></td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BCL6, BCL5, LAZ3, ZBTB27, ZNF51 ([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://proteopedia.org/fgij/fg.htm?mol=5h7g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h7g OCA], [http://pdbe.org/5h7g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5h7g RCSB], [http://www.ebi.ac.uk/pdbsum/5h7g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5h7g ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 21:		Line 22:
	</div>		</div>
	<div class="pdbe-citations 5h7g" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5h7g" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[B-cell lymphoma proteins 3D structures\|B-cell lymphoma proteins 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Ida, K]]		[[Category: Ida, K]]
	[[Category: Lane, W]]		[[Category: Lane, W]]

OCA: Protected "5h7g" [edit=sysop:move=sysop]

OCA — Fri, 09 Dec 2016 19:30:21 GMT

Protected "5h7g" [edit=sysop:move=sysop]

←Older revision

Revision as of 19:30, 9 December 2016

OCA: New page: ==Crystal structure of the BCL6 BTB domain in complex with F1324==
OCA — Fri, 09 Dec 2016 19:30:10 GMT

New page: ==Crystal structure of the BCL6 BTB domain in complex with F1324== <StructureSection load='5h7g' size='340' side='right' caption='5h7g, resolution 1.85Å' scene=''...

New page

==Crystal structure of the BCL6 BTB domain in complex with F1324==
<StructureSection load='5h7g' size='340' side='right' caption='[[5h7g]], [[Resolution|resolution]] 1.85Å' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5h7g]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5H7G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5H7G FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5h7h|5h7h]]</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=5h7g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5h7g OCA], [http://pdbe.org/5h7g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5h7g RCSB], [http://www.ebi.ac.uk/pdbsum/5h7g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5h7g ProSAT]</span></td></tr>
</table>
== Disease ==
[[http://www.uniprot.org/uniprot/BCL6_HUMAN BCL6_HUMAN]] Note=Chromosomal aberrations involving BCL6 may be a cause of B-cell non-Hodgkin lymphoma. Translocation t(3;14)(q27;q32); translocation t(3;22)(q27;q11) with immunoglobulin gene regions. Note=A chromosomal aberration involving BCL6 may be a cause of a form of B-cell leukemia. Translocation t(3;11)(q27;q23) with POU2AF1/OBF1. Note=A chromosomal aberration involving BCL6 may be a cause of lymphoma. Translocation t(3;4)(q27;p11) with ARHH/TTF.
== Function ==
[[http://www.uniprot.org/uniprot/BCL6_HUMAN BCL6_HUMAN]] Transcriptional repressor which is required for germinal center formation and antibody affinity maturation. Probably plays an important role in lymphomagenesis.<ref>PMID:9649500</ref> <ref>PMID:18280243</ref>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
B cell lymphoma 6 (BCL6) is a transcriptional repressor that interacts with its corepressors BcoR and SMRT. Since this protein-protein interaction (PPI) induces activation and differentiation of B lymphocytes, BCL6 has been an attractive drug target for potential autoimmune disease treatments. Here we report a novel BCL6 inhibitory peptide, F1324 (Ac-LWYTDIRMSWRVP-OH), which we discovered using phage display technology; we also discuss this peptide's structure-activity relationship (SAR). For BCL6(5-129) binding, KD and IC50 values of F1324 were 0.57 nM and 1 nM according to the results of an SPR analysis and cell-free ELISA assay, respectively. In contrast, BcoR(Arg498-514Pro) and SMRT(Leu1422-Arg1438) exhibited relatively weak micromole-order binding to BCL6. Furthermore, Fusion protein AcGFP-F1324 transiently expressed in HEK293T cells inhibited intracellular PPI in cell-based M2H assay. By examination of the truncation and fragmentation of F1324, the C-terminal sequence WRVP, which is similar to the BcoR(509-512) sequence WVVP, was identified as being critical for BCL6 binding. In addition, subsequent single-crystal X-ray diffraction analysis of F1324/BCL6(5-129) complex revealed that the high affinity of F1324 was caused by effective interaction of its side chains while its main chain structure was similar to that of BcoR(Arg498-514Pro). To our knowledge, F1324 is the strongest BCL6-binding peptide yet reported.

Discovery of high-affinity BCL6-binding peptide and its structure-activity relationship.,Sakamoto K, Sogabe S, Kamada Y, Sakai N, Asano K, Yoshimatsu M, Ida K, Imaeda Y, Sakamoto JI Biochem Biophys Res Commun. 2016 Nov 14. pii: S0006-291X(16)31916-7. doi:, 10.1016/j.bbrc.2016.11.060. PMID:27856253<ref>PMID:27856253</ref>

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5h7g" style="background-color:#fffaf0;"></div>
== References ==
<references/>
TOC
</StructureSection>
[[Category: Ida, K]]
[[Category: Lane, W]]
[[Category: Snell, G]]
[[Category: Sogabe, S]]
[[Category: Complex]]
[[Category: Inhibitor]]
[[Category: Transcription repressor]]
[[Category: Transcription-inhibitor complex]]