3hmf - Revision history

OCA at 15:50, 1 November 2023

OCA — Wed, 01 Nov 2023 15:50:44 GMT

←Older revision		Revision as of 15:50, 1 November 2023
Line 3:		Line 3:
	<StructureSection load='3hmf' size='340' side='right'caption='[[3hmf]], [[Resolution\|resolution]] 1.63Å' scene=''>		<StructureSection load='3hmf' size='340' side='right'caption='[[3hmf]], [[Resolution\|resolution]] 1.63Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3hmf]] is a 1 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=3HMF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3HMF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3hmf]] is a 1 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=3HMF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3HMF 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=EDO:~~1~~,2-ETHANEDIOL'>EDO</scene>, <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]] 1.63Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[3hme\|3hme]], [[3hmh\|3hmh]]~~</~~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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<~~tr id~~='~~gene'><td class~~=~~"sblockLbl"><b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">PB1, PBRM1 ([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'>[https://proteopedia.org/fgij/fg.htm?mol=3hmf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hmf OCA], [https://pdbe.org/3hmf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3hmf RCSB], [https://www.ebi.ac.uk/pdbsum/3hmf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3hmf 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=3hmf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hmf OCA], [https://pdbe.org/3hmf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3hmf RCSB], [https://www.ebi.ac.uk/pdbsum/3hmf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3hmf ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
-	[[https://www.uniprot.org/uniprot/PB1_HUMAN PB1_HUMAN]] Defects in PBRM1 are a cause of renal cell carcinoma (RCC) [MIM:[https://omim.org/entry/144700 144700]]. It is a heterogeneous group of sporadic or hereditary carcinoma derived from cells of the proximal renal tubular epithelium. It is subclassified into clear cell renal carcinoma (non-papillary carcinoma), papillary renal cell carcinoma, chromophobe renal cell carcinoma, collecting duct carcinoma with medullary carcinoma of the kidney, and unclassified renal cell carcinoma.<ref>PMID:21248752</ref>	+	[https://www.uniprot.org/uniprot/PB1_HUMAN PB1_HUMAN] Defects in PBRM1 are a cause of renal cell carcinoma (RCC) [MIM:[https://omim.org/entry/144700 144700]. It is a heterogeneous group of sporadic or hereditary carcinoma derived from cells of the proximal renal tubular epithelium. It is subclassified into clear cell renal carcinoma (non-papillary carcinoma), papillary renal cell carcinoma, chromophobe renal cell carcinoma, collecting duct carcinoma with medullary carcinoma of the kidney, and unclassified renal cell carcinoma.<ref>PMID:21248752</ref>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/PB1_HUMAN PB1_HUMAN]] Involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology). Acts as a negative regulator of cell proliferation.<ref>PMID:21248752</ref>	+	[https://www.uniprot.org/uniprot/PB1_HUMAN PB1_HUMAN] Involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology). Acts as a negative regulator of cell proliferation.<ref>PMID:21248752</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	__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: Delft, F von~~]]	+	[[Category: Edwards A]]
-	[[Category: Edwards, A]]	+	[[Category: Filippakopoulos P]]
-	[[Category: Filippakopoulos, P]]	+	[[Category: Keates T]]
-	[[Category: Keates, T]]	+	[[Category: Knapp S]]
-	[[Category: Knapp, S]]	+	[[Category: Muniz J]]
-	[[Category: Muniz, J]]	+	[[Category: Picaud S]]
-	[[Category: Picaud, S]]	+	[[Category: Weigelt J]]
-	~~[[Category: Structural genomic~~]]	+	[[Category: Von Delft F]]
-	[[Category: Weigelt, J]]	+
-	[[Category: ~~Baf180]]~~	+
-	~~[[Category: Brg1-associated factor 180]]~~	+
-	~~[[Category: Bromodomain]]~~	+
-	~~[[Category: Chromatin regulator]]~~	+
-	~~[[Category: Dna-binding]]~~	+
-	~~[[Category: Nucleus]]~~	+
-	~~[[Category: Pb1]]~~	+
-	~~[[Category: Pbrm1]]~~	+
-	~~[[Category: Phosphoprotein]]~~	+
-	~~[[Category: Polybromo 1 isoform 1]]~~	+
-	~~[[Category: Polybromo-1d]]~~	+
-	~~[[Category: Sgc]]~~	+
-	~~[[Category: Transcription]]~~	+
-	~~[[Category: Transcription regulation~~]]	+

OCA at 12:52, 23 March 2022

OCA — Wed, 23 Mar 2022 12:52:19 GMT

←Older revision		Revision as of 12:52, 23 March 2022
Line 1:		Line 1:

	==Crystal Structure of the second Bromodomain of Human Poly-bromodomain containing protein 1 (PB1)==		==Crystal Structure of the second Bromodomain of Human Poly-bromodomain containing protein 1 (PB1)==
-	<StructureSection load='3hmf' size='340' side='right' caption='[[3hmf]], [[Resolution\|resolution]] 1.63Å' scene=''>	+	<StructureSection load='3hmf' size='340' side='right'caption='[[3hmf]], [[Resolution\|resolution]] 1.63Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3hmf]] is a 1 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=3HMF OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3HMF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3hmf]] is a 1 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=3HMF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3HMF 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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <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" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3hme\|3hme]], [[3hmh\|3hmh]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3hme\|3hme]], [[3hmh\|3hmh]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PB1, PBRM1 ([~~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">PB1, PBRM1 ([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=3hmf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hmf OCA], [~~http~~://pdbe.org/3hmf PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3hmf RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3hmf PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3hmf 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=3hmf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hmf OCA], [https://pdbe.org/3hmf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3hmf RCSB], [https://www.ebi.ac.uk/pdbsum/3hmf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3hmf ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
-	[[~~http~~://www.uniprot.org/uniprot/PB1_HUMAN PB1_HUMAN]] Defects in PBRM1 are a cause of renal cell carcinoma (RCC) [MIM:[~~http~~://omim.org/entry/144700 144700]]. It is a heterogeneous group of sporadic or hereditary carcinoma derived from cells of the proximal renal tubular epithelium. It is subclassified into clear cell renal carcinoma (non-papillary carcinoma), papillary renal cell carcinoma, chromophobe renal cell carcinoma, collecting duct carcinoma with medullary carcinoma of the kidney, and unclassified renal cell carcinoma.<ref>PMID:21248752</ref>	+	[[https://www.uniprot.org/uniprot/PB1_HUMAN PB1_HUMAN]] Defects in PBRM1 are a cause of renal cell carcinoma (RCC) [MIM:[https://omim.org/entry/144700 144700]]. It is a heterogeneous group of sporadic or hereditary carcinoma derived from cells of the proximal renal tubular epithelium. It is subclassified into clear cell renal carcinoma (non-papillary carcinoma), papillary renal cell carcinoma, chromophobe renal cell carcinoma, collecting duct carcinoma with medullary carcinoma of the kidney, and unclassified renal cell carcinoma.<ref>PMID:21248752</ref>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/PB1_HUMAN PB1_HUMAN]] Involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology). Acts as a negative regulator of cell proliferation.<ref>PMID:21248752</ref>	+	[[https://www.uniprot.org/uniprot/PB1_HUMAN PB1_HUMAN]] Involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology). Acts as a negative regulator of cell proliferation.<ref>PMID:21248752</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 37:		Line 37:
	</StructureSection>		</StructureSection>
	[[Category: Human]]		[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Arrowsmith, C H]]		[[Category: Arrowsmith, C H]]
	[[Category: Bountra, C]]		[[Category: Bountra, C]]

OCA at 07:43, 12 December 2018

OCA — Wed, 12 Dec 2018 07:43:52 GMT

←Older revision		Revision as of 07:43, 12 December 2018
Line 1:		Line 1:
		+
	==Crystal Structure of the second Bromodomain of Human Poly-bromodomain containing protein 1 (PB1)==		==Crystal Structure of the second Bromodomain of Human Poly-bromodomain containing protein 1 (PB1)==
	<StructureSection load='3hmf' size='340' side='right' caption='[[3hmf]], [[Resolution\|resolution]] 1.63Å' scene=''>		<StructureSection load='3hmf' size='340' side='right' caption='[[3hmf]], [[Resolution\|resolution]] 1.63Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3hme\|3hme]], [[3hmh\|3hmh]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3hme\|3hme]], [[3hmh\|3hmh]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PB1, PBRM1 ([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">PB1, PBRM1 ([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=3hmf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hmf OCA], [http://pdbe.org/3hmf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3hmf RCSB], [http://www.ebi.ac.uk/pdbsum/3hmf 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=3hmf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hmf OCA], [http://pdbe.org/3hmf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3hmf RCSB], [http://www.ebi.ac.uk/pdbsum/3hmf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3hmf ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 16:		Line 17:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hm/3hmf_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hm/3hmf_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>
Line 45:		Line 46:
	[[Category: Muniz, J]]		[[Category: Muniz, J]]
	[[Category: Picaud, S]]		[[Category: Picaud, S]]
		+	[[Category: Structural genomic]]
	[[Category: Weigelt, J]]		[[Category: Weigelt, J]]
	[[Category: Baf180]]		[[Category: Baf180]]
Line 58:		Line 60:
	[[Category: Polybromo-1d]]		[[Category: Polybromo-1d]]
	[[Category: Sgc]]		[[Category: Sgc]]
-	[[Category: Structural genomic]]
	[[Category: Transcription]]		[[Category: Transcription]]
	[[Category: Transcription regulation]]		[[Category: Transcription regulation]]

OCA at 20:17, 7 February 2016

OCA — Sun, 07 Feb 2016 20:17:58 GMT

←Older revision		Revision as of 20:17, 7 February 2016
Line 2:		Line 2:
	<StructureSection load='3hmf' size='340' side='right' caption='[[3hmf]], [[Resolution\|resolution]] 1.63Å' scene=''>		<StructureSection load='3hmf' size='340' side='right' caption='[[3hmf]], [[Resolution\|resolution]] 1.63Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3hmf]] is a 1 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=3HMF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3HMF FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3hmf]] is a 1 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=3HMF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3HMF 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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3hme\|3hme]], [[3hmh\|3hmh]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3hme\|3hme]], [[3hmh\|3hmh]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PB1, PBRM1 ([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">PB1, PBRM1 ([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=3hmf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hmf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3hmf RCSB], [http://www.ebi.ac.uk/pdbsum/3hmf 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=3hmf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hmf OCA], [http://pdbe.org/3hmf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3hmf RCSB], [http://www.ebi.ac.uk/pdbsum/3hmf PDBsum]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==
Line 20:		Line 20:
	<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=3hmf ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 30:		Line 30:
	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 3hmf" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Homo sapiens~~]]	+	[[Category: Human]]
	[[Category: Arrowsmith, C H]]		[[Category: Arrowsmith, C H]]
	[[Category: Bountra, C]]		[[Category: Bountra, C]]

OCA at 15:53, 18 December 2014

OCA — Thu, 18 Dec 2014 15:53:51 GMT

←Older revision		Revision as of 15:53, 18 December 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_3hmf\| PDB=3hmf \| SCENE= }}~~	+	==Crystal Structure of the second Bromodomain of Human Poly-bromodomain containing protein 1 (PB1)==
-	===Crystal Structure of the second Bromodomain of Human Poly-bromodomain containing protein 1 (PB1)===	+	<StructureSection load='3hmf' size='340' side='right' caption='[[3hmf]], [[Resolution\|resolution]] 1.63Å' scene=''>
-	~~{{ABSTRACT_PUBMED_22464331}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3hmf]] is a 1 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=3HMF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3HMF 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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3hme\|3hme]], [[3hmh\|3hmh]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">PB1, PBRM1 ([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=3hmf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hmf OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3hmf RCSB], [http://www.ebi.ac.uk/pdbsum/3hmf PDBsum]</span></td></tr>
		+	</table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/PB1_HUMAN PB1_HUMAN]] Defects in PBRM1 are a cause of renal cell carcinoma (RCC) [MIM:[http://omim.org/entry/144700 144700]]. It is a heterogeneous group of sporadic or hereditary carcinoma derived from cells of the proximal renal tubular epithelium. It is subclassified into clear cell renal carcinoma (non-papillary carcinoma), papillary renal cell carcinoma, chromophobe renal cell carcinoma, collecting duct carcinoma with medullary carcinoma of the kidney, and unclassified renal cell carcinoma.<ref>PMID:21248752</ref>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/PB1_HUMAN PB1_HUMAN]] Involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology). Acts as a negative regulator of cell proliferation.<ref>PMID:21248752</ref>
		+	== 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/hm/3hmf_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 ==
		+	Bromodomains (BRDs) are protein interaction modules that specifically recognize epsilon-N-lysine acetylation motifs, a key event in the reading process of epigenetic marks. The 61 BRDs in the human genome cluster into eight families based on structure/sequence similarity. Here, we present 29 high-resolution crystal structures, covering all BRD families. Comprehensive crossfamily structural analysis identifies conserved and family-specific structural features that are necessary for specific acetylation-dependent substrate recognition. Screening of more than 30 representative BRDs against systematic histone-peptide arrays identifies new BRD substrates and reveals a strong influence of flanking posttranslational modifications, such as acetylation and phosphorylation, suggesting that BRDs recognize combinations of marks rather than singly acetylated sequences. We further uncovered a structural mechanism for the simultaneous binding and recognition of diverse diacetyl-containing peptides by BRD4. These data provide a foundation for structure-based drug design of specific inhibitors for this emerging target family.

-	~~==Disease==~~	+	Histone recognition and large-scale structural analysis of the human bromodomain family.,Filippakopoulos P, Picaud S, Mangos M, Keates T, Lambert JP, Barsyte-Lovejoy D, Felletar I, Volkmer R, Muller S, Pawson T, Gingras AC, Arrowsmith CH, Knapp S Cell. 2012 Mar 30;149(1):214-31. PMID:22464331<ref>PMID:22464331</ref>
-	[[http://www.uniprot.org/uniprot/PB1_HUMAN PB1_HUMAN]] Defects in PBRM1 are a cause of renal cell carcinoma (RCC) [MIM:[http://omim.org/entry/144700 144700]]. It is a heterogeneous group of sporadic or hereditary carcinoma derived from cells of the ~~proximal renal tubular epithelium~~. ~~It is subclassified into clear cell renal carcinoma (non~~-~~papillary carcinoma)~~, ~~papillary renal cell carcinoma~~, ~~chromophobe renal cell carcinoma~~, ~~collecting duct carcinoma with medullary carcinoma of the kidney~~, ~~and unclassified renal cell carcinoma~~.<ref>PMID:~~21248752~~</ref>	+

-	~~==Function==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[http:~~/~~/www~~.~~uniprot~~.~~org/uniprot/PB1_HUMAN PB1_HUMAN]] Involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration~~ of ~~DNA-nucleosome topology). Acts as a negative regulator of cell proliferation~~.<~~ref~~>~~PMID:21248752~~</~~ref~~>	+	</div>
-		+	== References ==
-	==~~About this Structure==~~	+	<references/>
-	[[3hmf]] is a 1 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=3HMF OCA].	+	__TOC__
-		+	</StructureSection>
-	~~==Reference~~==	+
-	~~<ref group="xtra">PMID:022464331</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
-	[[Category: Arrowsmith, C H.]]	+	[[Category: Arrowsmith, C H]]
-	[[Category: Bountra, C.]]	+	[[Category: Bountra, C]]
-	[[Category: Delft, F von.]]	+	[[Category: Delft, F von]]
-	[[Category: Edwards, A.]]	+	[[Category: Edwards, A]]
-	[[Category: Filippakopoulos, P.]]	+	[[Category: Filippakopoulos, P]]
-	[[Category: Keates, T.]]	+	[[Category: Keates, T]]
-	[[Category: Knapp, S.]]	+	[[Category: Knapp, S]]
-	[[Category: Muniz, J.]]	+	[[Category: Muniz, J]]
-	[[Category: Picaud, S.]]	+	[[Category: Picaud, S]]
-	[[Category: Weigelt, J.]]	+	[[Category: Weigelt, J]]
	[[Category: Baf180]]		[[Category: Baf180]]
	[[Category: Brg1-associated factor 180]]		[[Category: Brg1-associated factor 180]]
Line 38:		Line 58:
	[[Category: Sgc]]		[[Category: Sgc]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
-	[[Category: Structural genomics consortium]]
	[[Category: Transcription]]		[[Category: Transcription]]
	[[Category: Transcription regulation]]		[[Category: Transcription regulation]]

OCA at 23:56, 24 March 2013

OCA — Sun, 24 Mar 2013 23:56:42 GMT

←Older revision		Revision as of 23:56, 24 March 2013
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-	[[Image:3hmf.png\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_3hmf", 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_3hmf\| PDB=3hmf \| SCENE= }}		{{STRUCTURE_3hmf\| PDB=3hmf \| SCENE= }}
-
	===Crystal Structure of the second Bromodomain of Human Poly-bromodomain containing protein 1 (PB1)===		===Crystal Structure of the second Bromodomain of Human Poly-bromodomain containing protein 1 (PB1)===
		+	{{ABSTRACT_PUBMED_22464331}}

		+	==Disease==
		+	[[http://www.uniprot.org/uniprot/PB1_HUMAN PB1_HUMAN]] Defects in PBRM1 are a cause of renal cell carcinoma (RCC) [MIM:[http://omim.org/entry/144700 144700]]. It is a heterogeneous group of sporadic or hereditary carcinoma derived from cells of the proximal renal tubular epithelium. It is subclassified into clear cell renal carcinoma (non-papillary carcinoma), papillary renal cell carcinoma, chromophobe renal cell carcinoma, collecting duct carcinoma with medullary carcinoma of the kidney, and unclassified renal cell carcinoma.<ref>PMID:21248752</ref>

-	~~<!--~~	+	==Function==
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_22464331}}, adds the Publication Abstract to the page~~	+	[[http://www.uniprot.org/uniprot/PB1_HUMAN PB1_HUMAN]] Involved in transcriptional activation and repression of select genes by chromatin remodeling (alteration of DNA-nucleosome topology). Acts as a negative regulator of cell proliferation.<ref>PMID:21248752</ref>
-	~~(as it appears on PubMed at~~ http://www.~~pubmed~~.~~gov~~)~~, where 22464331 is the PubMed ID number~~.	+
-	-->	+
-	~~{{ABSTRACT_PUBMED_22464331}}~~	+

	==About this Structure==		==About this Structure==
Line 22:		Line 13:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:022464331</ref><references group="xtra"/>	+	<ref group="xtra">PMID:022464331</ref><references group="xtra"/><references/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Arrowsmith, C H.]]		[[Category: Arrowsmith, C H.]]

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

OCA — Wed, 11 Apr 2012 06:14:15 GMT

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

←Older revision

Revision as of 06:14, 11 April 2012

OCA at 06:14, 11 April 2012

OCA — Wed, 11 Apr 2012 06:14:13 GMT

←Older revision		Revision as of 06:14, 11 April 2012
Line 1:		Line 1:
-	~~{{Seed}}~~	+	[[Image:3hmf.png\|left\|200px]]
-	[[Image:3hmf.~~jpg~~\|left\|200px]]	+

	<!--		<!--
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	===Crystal Structure of the second Bromodomain of Human Poly-bromodomain containing protein 1 (PB1)===		===Crystal Structure of the second Bromodomain of Human Poly-bromodomain containing protein 1 (PB1)===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_22464331}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 22464331 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_22464331}}

	==About this Structure==		==About this Structure==
-	~~3HMF~~ is a 1 chain structure of 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=3HMF OCA].	+	[[3hmf]] is a 1 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=3HMF OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:022464331</ref><references group="xtra"/>
	[[Category: Homo sapiens]]		[[Category: Homo sapiens]]
	[[Category: Arrowsmith, C H.]]		[[Category: Arrowsmith, C H.]]
Line 26:		Line 34:
	[[Category: Picaud, S.]]		[[Category: Picaud, S.]]
	[[Category: Weigelt, J.]]		[[Category: Weigelt, J.]]
-	[[Category: Alternative splicing]]
	[[Category: Baf180]]		[[Category: Baf180]]
	[[Category: Brg1-associated factor 180]]		[[Category: Brg1-associated factor 180]]
Line 43:		Line 50:
	[[Category: Transcription]]		[[Category: Transcription]]
	[[Category: Transcription regulation]]		[[Category: Transcription regulation]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jun 25 11:26:01 2009''

OCA at 08:26, 25 June 2009

OCA — Thu, 25 Jun 2009 08:26:02 GMT

←Older revision		Revision as of 08:26, 25 June 2009
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-	~~'''Unreleased structure'''~~	+	{{Seed}}
		+	[[Image:3hmf.jpg\|left\|200px]]

-	The ~~entry 3hmf~~ is ~~ON HOLD~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3hmf", 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_3hmf\| PDB=3hmf \| SCENE= }}

-	~~Authors: Filippakopoulos, P., Picaud, S., Keates, T., Muniz, J., von Delft, F., Arrowsmith, C.H., Edwards, A., Weigelt, J., Bountra, C., Knapp, S.~~	+	===Crystal Structure of the second Bromodomain of Human Poly-bromodomain containing protein 1 (PB1)===

-	Description: Crystal Structure of the second Bromodomain of Human Poly-bromodomain containing protein 1 (PB1)

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Wed~~ Jun ~~17 09~~:46:37 2009''	+	==About this Structure==
		+	3HMF is a 1 chain structure of 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=3HMF OCA].
		+	[[Category: Homo sapiens]]
		+	[[Category: Arrowsmith, C H.]]
		+	[[Category: Bountra, C.]]
		+	[[Category: Delft, F von.]]
		+	[[Category: Edwards, A.]]
		+	[[Category: Filippakopoulos, P.]]
		+	[[Category: Keates, T.]]
		+	[[Category: Knapp, S.]]
		+	[[Category: Muniz, J.]]
		+	[[Category: Picaud, S.]]
		+	[[Category: Weigelt, J.]]
		+	[[Category: Alternative splicing]]
		+	[[Category: Baf180]]
		+	[[Category: Brg1-associated factor 180]]
		+	[[Category: Bromodomain]]
		+	[[Category: Chromatin regulator]]
		+	[[Category: Dna-binding]]
		+	[[Category: Nucleus]]
		+	[[Category: Pb1]]
		+	[[Category: Pbrm1]]
		+	[[Category: Phosphoprotein]]
		+	[[Category: Polybromo 1 isoform 1]]
		+	[[Category: Polybromo-1d]]
		+	[[Category: Sgc]]
		+	[[Category: Structural genomic]]
		+	[[Category: Structural genomics consortium]]
		+	[[Category: Transcription]]
		+	[[Category: Transcription regulation]]
		+
		+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jun 25 11:26:01 2009''

OCA at 06:46, 17 June 2009

OCA — Wed, 17 Jun 2009 06:46:38 GMT

←Older revision		Revision as of 06:46, 17 June 2009
Line 3:		Line 3:
	The entry 3hmf is ON HOLD		The entry 3hmf is ON HOLD

-	Authors: Filippakopoulos, P., Picaud, S., Keates, T., Muniz, J., von Delft, F., Arrowsmith, C.H., Edwards, A., Weigelt, J., Bountra, C., Knapp, S.~~, Structural Genomics Consortium (SGC)~~	+	Authors: Filippakopoulos, P., Picaud, S., Keates, T., Muniz, J., von Delft, F., Arrowsmith, C.H., Edwards, A., Weigelt, J., Bountra, C., Knapp, S.

	Description: Crystal Structure of the second Bromodomain of Human Poly-bromodomain containing protein 1 (PB1)		Description: Crystal Structure of the second Bromodomain of Human Poly-bromodomain containing protein 1 (PB1)

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jun 10 17:59:54 2009''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jun 17 09:46:37 2009''