3mb4

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Line 1: Line 1:
-
{{STRUCTURE_3mb4| PDB=3mb4 | SCENE= }}
+
==Crystal Structure of the fifth Bromodomain of Human Poly-bromodomain containing protein 1 (PB1) with NMP==
-
===Crystal Structure of the fifth Bromodomain of Human Poly-bromodomain containing protein 1 (PB1) with NMP===
+
<StructureSection load='3mb4' size='340' side='right' caption='[[3mb4]], [[Resolution|resolution]] 1.66&Aring;' scene=''>
-
{{ABSTRACT_PUBMED_22464331}}
+
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[3mb4]] is a 2 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=3MB4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3MB4 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=MB3:1-METHYLPYRROLIDIN-2-ONE'>MB3</scene></td></tr>
 +
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3mb3|3mb3]]</td></tr>
 +
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">BAF180, 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=3mb4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3mb4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3mb4 RCSB], [http://www.ebi.ac.uk/pdbsum/3mb4 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/mb/3mb4_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&reg;/PubMed&reg;, 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/>
-
[[3mb4]] is a 2 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=3MB4 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 M.]]
+
[[Category: Edwards, A M]]
-
[[Category: Filippakopoulos, P.]]
+
[[Category: Filippakopoulos, P]]
-
[[Category: Keates, T.]]
+
[[Category: Keates, T]]
-
[[Category: Knapp, S.]]
+
[[Category: Knapp, S]]
-
[[Category: Picaud, S.]]
+
[[Category: Picaud, S]]
-
[[Category: SGC, Structural Genomics Consortium.]]
+
[[Category: Structural genomic]]
-
[[Category: Ugochukwu, E.]]
+
[[Category: Ugochukwu, E]]
-
[[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: Polybromo-1d]]
[[Category: Polybromo-1d]]
[[Category: Sgc]]
[[Category: Sgc]]
-
[[Category: Structural genomics consortium]]
 
[[Category: Transcription]]
[[Category: Transcription]]
[[Category: Transcription regulation]]
[[Category: Transcription regulation]]

Revision as of 16:41, 18 December 2014

Crystal Structure of the fifth Bromodomain of Human Poly-bromodomain containing protein 1 (PB1) with NMP

3mb4, resolution 1.66Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3mb4"
Personal tools