6bw3 - Revision history

OCA at 14:51, 4 October 2023

OCA — Wed, 04 Oct 2023 14:51:20 GMT

←Older revision		Revision as of 14:51, 4 October 2023
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	<StructureSection load='6bw3' size='340' side='right'caption='[[6bw3]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='6bw3' size='340' side='right'caption='[[6bw3]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6bw3]] 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=6BW3 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6BW3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6bw3]] is a 4 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=6BW3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6BW3 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</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]] 2.2Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~RBBP4, RBAP48 ([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=UNX:UNKNOWN+ATOM+OR+ION'>UNX</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=6bw3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bw3 OCA], [~~http~~://pdbe.org/6bw3 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6bw3 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6bw3 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6bw3 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=6bw3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bw3 OCA], [https://pdbe.org/6bw3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6bw3 RCSB], [https://www.ebi.ac.uk/pdbsum/6bw3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6bw3 ProSAT]</span></td></tr>
	</table>		</table>
-	== Disease ==
-	[[http://www.uniprot.org/uniprot/MDS1_HUMAN MDS1_HUMAN]] A chromosomal aberration involving MDS1 is found in a form of acute myeloid leukemia (AML). Translocation t(3;21) with AML1.<ref>PMID:8643684</ref>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/RBBP4_HUMAN RBBP4_HUMAN]] Core histone-binding subunit that may target chromatin assembly factors, chromatin remodeling factors and histone deacetylases to their histone substrates in a manner that is regulated by nucleosomal DNA. Component of several complexes which regulate chromatin metabolism. These include the chromatin assembly factor 1 (CAF-1) complex, which is required for chromatin assembly following DNA replication and DNA repair; the core histone deacetylase (HDAC) complex, which promotes histone deacetylation and consequent transcriptional repression; the nucleosome remodeling and histone deacetylase complex (the NuRD complex), which promotes transcriptional repression by histone deacetylation and nucleosome remodeling; the PRC2/EED-EZH2 complex, which promotes repression of homeotic genes during development; and the NURF (nucleosome remodeling factor) complex.<ref>PMID:10866654</ref>	+	[https://www.uniprot.org/uniprot/RBBP4_HUMAN RBBP4_HUMAN] Core histone-binding subunit that may target chromatin assembly factors, chromatin remodeling factors and histone deacetylases to their histone substrates in a manner that is regulated by nucleosomal DNA. Component of several complexes which regulate chromatin metabolism. These include the chromatin assembly factor 1 (CAF-1) complex, which is required for chromatin assembly following DNA replication and DNA repair; the core histone deacetylase (HDAC) complex, which promotes histone deacetylation and consequent transcriptional repression; the nucleosome remodeling and histone deacetylase complex (the NuRD complex), which promotes transcriptional repression by histone deacetylation and nucleosome remodeling; the PRC2/EED-EZH2 complex, which promotes repression of homeotic genes during development; and the NURF (nucleosome remodeling factor) complex.<ref>PMID:10866654</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	==See Also==		==See Also==
-	*[[Retinoblastoma-binding protein\|Retinoblastoma-binding protein]]	+	*[[Retinoblastoma-binding protein 3D structures\|Retinoblastoma-binding protein 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Arrowsmith~~, C H~~]]	+	[[Category: Arrowsmith CH]]
-	[[Category: Bountra, C]]	+	[[Category: Bountra C]]
-	[[Category: Edwards~~, A M~~]]	+	[[Category: Edwards AM]]
-	[[Category: Halabelian, L]]	+	[[Category: Halabelian L]]
-	[[Category: Hutchinson, A]]	+	[[Category: Hutchinson A]]
-	[[Category: Ivanochko, D]]	+	[[Category: Ivanochko D]]
-	~~[[Category: Structural genomic~~]]	+	[[Category: Seitova A]]
-	[[Category: Seitova, A]]	+
-	~~[[Category: Chromatin regulator]]~~	+
-	~~[[Category: Complex]]~~	+
-	~~[[Category: Epigenetic]]~~	+
-	~~[[Category: Gene regulation]]~~	+
-	~~[[Category: Histone-binding protein]]~~	+
-	~~[[Category: Nucleus]]~~	+
-	~~[[Category: Nurd]]~~	+
-	~~[[Category: Repressor]]~~	+
-	~~[[Category: Sgc]]~~	+
-	~~[[Category: Wd repeat~~]]	+

OCA at 05:59, 10 October 2019

OCA — Thu, 10 Oct 2019 05:59:17 GMT

←Older revision		Revision as of 05:59, 10 October 2019
Line 1:		Line 1:

	==Crystal structure of RBBP4 in complex with PRDM3 N-terminal peptide==		==Crystal structure of RBBP4 in complex with PRDM3 N-terminal peptide==
-	<StructureSection load='6bw3' size='340' side='right' caption='[[6bw3]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='6bw3' size='340' side='right'caption='[[6bw3]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6bw3]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BW3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BW3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6bw3]] 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=6BW3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BW3 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">RBBP4, RBAP48 ([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=6bw3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bw3 OCA], [http://pdbe.org/6bw3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6bw3 RCSB], [http://www.ebi.ac.uk/pdbsum/6bw3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6bw3 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=6bw3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bw3 OCA], [http://pdbe.org/6bw3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6bw3 RCSB], [http://www.ebi.ac.uk/pdbsum/6bw3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6bw3 ProSAT]</span></td></tr>
	</table>		</table>
Line 11:		Line 12:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/RBBP4_HUMAN RBBP4_HUMAN]] Core histone-binding subunit that may target chromatin assembly factors, chromatin remodeling factors and histone deacetylases to their histone substrates in a manner that is regulated by nucleosomal DNA. Component of several complexes which regulate chromatin metabolism. These include the chromatin assembly factor 1 (CAF-1) complex, which is required for chromatin assembly following DNA replication and DNA repair; the core histone deacetylase (HDAC) complex, which promotes histone deacetylation and consequent transcriptional repression; the nucleosome remodeling and histone deacetylase complex (the NuRD complex), which promotes transcriptional repression by histone deacetylation and nucleosome remodeling; the PRC2/EED-EZH2 complex, which promotes repression of homeotic genes during development; and the NURF (nucleosome remodeling factor) complex.<ref>PMID:10866654</ref>		[[http://www.uniprot.org/uniprot/RBBP4_HUMAN RBBP4_HUMAN]] Core histone-binding subunit that may target chromatin assembly factors, chromatin remodeling factors and histone deacetylases to their histone substrates in a manner that is regulated by nucleosomal DNA. Component of several complexes which regulate chromatin metabolism. These include the chromatin assembly factor 1 (CAF-1) complex, which is required for chromatin assembly following DNA replication and DNA repair; the core histone deacetylase (HDAC) complex, which promotes histone deacetylation and consequent transcriptional repression; the nucleosome remodeling and histone deacetylase complex (the NuRD complex), which promotes transcriptional repression by histone deacetylation and nucleosome remodeling; the PRC2/EED-EZH2 complex, which promotes repression of homeotic genes during development; and the NURF (nucleosome remodeling factor) complex.<ref>PMID:10866654</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Aberrant isoform expression of chromatin-associated proteins can induce epigenetic programs related to disease. The MDS1 and EVI1 complex locus (MECOM) encodes PRDM3, a protein with an N-terminal PR-SET domain, as well as a shorter isoform, EVI1, lacking the N-terminus containing the PR-SET domain (DeltaPR). Imbalanced expression of MECOM isoforms is observed in multiple malignancies, implicating EVI1 as an oncogene, while PRDM3 has been suggested to function as a tumor suppressor through an unknown mechanism. To elucidate functional characteristics of these N-terminal residues, we compared the protein interactomes of the full-length and DeltaPR isoforms of PRDM3 and its closely related paralog, PRDM16. Unlike the DeltaPR isoforms, both full-length isoforms exhibited a significantly enriched association with components of the NuRD chromatin remodeling complex, especially RBBP4. Typically, RBBP4 facilitates chromatin association of the NuRD complex by binding to histone H3 tails. We show that RBBP4 binds to the N-terminal amino acid residues of PRDM3 and PRDM16, with a dissociation constant of 3.0 muM, as measured by isothermal titration calorimetry. Furthermore, high-resolution X-ray crystal structures of PRDM3 and PRDM16 N-terminal peptides in complex with RBBP4 revealed binding to RBBP4 within the conserved histone H3-binding groove. These data support a mechanism of isoform-specific interaction of PRDM3 and PRDM16 with the NuRD chromatin remodeling complex.
		+
		+	Direct interaction between the PRDM3 and PRDM16 tumor suppressors and the NuRD chromatin remodeling complex.,Ivanochko D, Halabelian L, Henderson E, Savitsky P, Jain H, Marcon E, Duan S, Hutchinson A, Seitova A, Barsyte-Lovejoy D, Filippakopoulos P, Greenblatt J, Lima-Fernandes E, Arrowsmith CH Nucleic Acids Res. 2019 Feb 20;47(3):1225-1238. doi: 10.1093/nar/gky1192. PMID:30462309<ref>PMID:30462309</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6bw3" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Retinoblastoma-binding protein\|Retinoblastoma-binding protein]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Arrowsmith, C H]]		[[Category: Arrowsmith, C H]]
	[[Category: Bountra, C]]		[[Category: Bountra, C]]

OCA at 08:39, 27 December 2017

OCA — Wed, 27 Dec 2017 08:39:52 GMT

←Older revision		Revision as of 08:39, 27 December 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6bw3 is ~~ON HOLD~~	+	==Crystal structure of RBBP4 in complex with PRDM3 N-terminal peptide==
-		+	<StructureSection load='6bw3' size='340' side='right' caption='[[6bw3]], [[Resolution\|resolution]] 2.20Å' scene=''>
-	~~Authors~~: ~~Ivanochko, D~~.~~, Halabelian, L~~.~~, Hutchinson, A~~., ~~Seitova, A~~., ~~Bountra, C~~., ~~Edwards, A~~.M., ~~Arrowsmith, C~~.H., ~~Structural Genomics Consortium, Structural Genomics Consortium~~ (~~SGC~~)	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6bw3]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6BW3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6BW3 FirstGlance]. <br>
-	~~Description~~: ~~Crystal structure of RBBP4~~ in complex ~~with PRDM3 N~~-~~terminal peptide~~.	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNX:UNKNOWN+ATOM+OR+ION'>UNX</scene></td></tr>
-	[[Category: ~~Unreleased Structures~~]]	+	<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=6bw3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6bw3 OCA], [http://pdbe.org/6bw3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6bw3 RCSB], [http://www.ebi.ac.uk/pdbsum/6bw3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6bw3 ProSAT]</span></td></tr>
		+	</table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/MDS1_HUMAN MDS1_HUMAN]] A chromosomal aberration involving MDS1 is found in a form of acute myeloid leukemia (AML). Translocation t(3;21) with AML1.<ref>PMID:8643684</ref>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/RBBP4_HUMAN RBBP4_HUMAN]] Core histone-binding subunit that may target chromatin assembly factors, chromatin remodeling factors and histone deacetylases to their histone substrates in a manner that is regulated by nucleosomal DNA. Component of several complexes which regulate chromatin metabolism. These include the chromatin assembly factor 1 (CAF-1) complex, which is required for chromatin assembly following DNA replication and DNA repair; the core histone deacetylase (HDAC) complex, which promotes histone deacetylation and consequent transcriptional repression; the nucleosome remodeling and histone deacetylase complex (the NuRD complex), which promotes transcriptional repression by histone deacetylation and nucleosome remodeling; the PRC2/EED-EZH2 complex, which promotes repression of homeotic genes during development; and the NURF (nucleosome remodeling factor) complex.<ref>PMID:10866654</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Arrowsmith, C H]]
		+	[[Category: Bountra, C]]
		+	[[Category: Edwards, A M]]
		+	[[Category: Halabelian, L]]
	[[Category: Hutchinson, A]]		[[Category: Hutchinson, A]]
-	[[Category: ~~Arrowsmith~~, ~~C.H~~]]	+	[[Category: Ivanochko, D]]
		+	[[Category: Structural genomic]]
	[[Category: Seitova, A]]		[[Category: Seitova, A]]
-	[[Category: ~~Halabelian, L~~]]	+	[[Category: Chromatin regulator]]
-	[[Category: ~~Structural Genomics Consortium, Structural Genomics Consortium (Sgc)~~]]	+	[[Category: Complex]]
-	[[Category: ~~Ivanochko, D~~]]	+	[[Category: Epigenetic]]
-	[[Category: ~~Edwards, A.M~~]]	+	[[Category: Gene regulation]]
-	[[Category: ~~Bountra, C~~]]	+	[[Category: Histone-binding protein]]
		+	[[Category: Nucleus]]
		+	[[Category: Nurd]]
		+	[[Category: Repressor]]
		+	[[Category: Sgc]]
		+	[[Category: Wd repeat]]

OCA: Protected "6bw3" [edit=sysop:move=sysop]

OCA — Wed, 20 Dec 2017 05:05:06 GMT

Protected "6bw3" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:05, 20 December 2017

OCA: New page: '''Unreleased structure''' The entry 6bw3 is ON HOLD Authors: Ivanochko, D., Halabelian, L., Hutchinson, A., Seitova, A., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Structural Genomi...

OCA — Wed, 20 Dec 2017 05:05:05 GMT

New page: '''Unreleased structure''' The entry 6bw3 is ON HOLD Authors: Ivanochko, D., Halabelian, L., Hutchinson, A., Seitova, A., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Structural Genomi...

New page

'''Unreleased structure'''

The entry 6bw3 is ON HOLD

Authors: Ivanochko, D., Halabelian, L., Hutchinson, A., Seitova, A., Bountra, C., Edwards, A.M., Arrowsmith, C.H., Structural Genomics Consortium, Structural Genomics Consortium (SGC)

Description: Crystal structure of RBBP4 in complex with PRDM3 N-terminal peptide.
[[Category: Unreleased Structures]]
[[Category: Hutchinson, A]]
[[Category: Arrowsmith, C.H]]
[[Category: Seitova, A]]
[[Category: Halabelian, L]]
[[Category: Structural Genomics Consortium, Structural Genomics Consortium (Sgc)]]
[[Category: Ivanochko, D]]
[[Category: Edwards, A.M]]
[[Category: Bountra, C]]