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3dm1

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[[Image:3dm1.png|left|200px]]
 
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{{STRUCTURE_3dm1| PDB=3dm1 | SCENE= }}
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==Crystal structure of the complex of human chromobox homolog 3 (CBX3) with peptide==
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<StructureSection load='3dm1' size='340' side='right'caption='[[3dm1]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[3dm1]] is a 8 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=3DM1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DM1 FirstGlance]. <br>
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</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">CBX3 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3dm1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dm1 OCA], [https://pdbe.org/3dm1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dm1 RCSB], [https://www.ebi.ac.uk/pdbsum/3dm1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dm1 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[[https://www.uniprot.org/uniprot/CBX3_HUMAN CBX3_HUMAN]] Seems to be involved in transcriptional silencing in heterochromatin-like complexes. Recognizes and binds histone H3 tails methylated at 'Lys-9', leading to epigenetic repression. May contribute to the association of the heterochromatin with the inner nuclear membrane through its interaction with lamin B receptor (LBR). Involved in the formation of functional kinetochore through interaction with MIS12 complex proteins. [[https://www.uniprot.org/uniprot/EHMT2_HUMAN EHMT2_HUMAN]] Histone methyltransferase that specifically mono- and dimethylates 'Lys-9' of histone H3 (H3K9me1 and H3K9me2, respectively) in euchromatin. H3K9me represents a specific tag for epigenetic transcriptional repression by recruiting HP1 proteins to methylated histones. Also mediates monomethylation of 'Lys-56' of histone H3 (H3K56me1) in G1 phase, leading to promote interaction between histone H3 and PCNA and regulating DNA replication. Also weakly methylates 'Lys-27' of histone H3 (H3K27me). Also required for DNA methylation, the histone methyltransferase activity is not required for DNA methylation, suggesting that these 2 activities function independently. Probably targeted to histone H3 by different DNA-binding proteins like E2F6, MGA, MAX and/or DP1. May also methylate histone H1. In addition to the histone methyltransferase activity, also methylates non-histone proteins: mediates dimethylation of 'Lys-373' of p53/TP53. Also methylates CDYL, WIZ, ACIN1, DNMT1, HDAC1, ERCC6, KLF12 and itself.<ref>PMID:8457211</ref> <ref>PMID:11316813</ref> <ref>PMID:18438403</ref> <ref>PMID:20118233</ref> <ref>PMID:22387026</ref>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dm/3dm1_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=3dm1 ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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BACKGROUND: HP1 proteins are highly conserved heterochromatin proteins, which have been identified to be structural adapters assembling a variety of macromolecular complexes involved in regulation of gene expression, chromatin remodeling and heterochromatin formation. Much evidence shows that HP1 proteins interact with numerous proteins including methylated histones, histone methyltransferases and so on. Cbx3 is one of the paralogues of HP1 proteins, which has been reported to specifically recognize trimethylated histone H3K9 mark, and a consensus binding motif has been defined for the Cbx3 chromodomain. METHODOLOGY/PRINCIPAL FINDINGS: Here, we found that the Cbx3 chromodomain can bind to H1K26me2 and G9aK185me3 with comparable binding affinities compared to H3K9me3. We also determined the crystal structures of the human Cbx3 chromodomain in complex with dimethylated histone H1K26 and trimethylated G9aK185 peptides, respectively. The complex structures unveil that the Cbx3 chromodomain specifically bind methylated histone H1K26 and G9aK185 through a conserved mechanism. CONCLUSIONS/SIGNIFICANCE: The Cbx3 chromodomain binds with comparable affinities to all of the methylated H3K9, H1K26 and G9aK185 peptides. It is suggested that Cbx3 may regulate gene expression via recognizing both histones and non-histone proteins.
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===Crystal structure of the complex of human chromobox homolog 3 (CBX3) with peptide===
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Structural basis of the chromodomain of Cbx3 bound to methylated peptides from histone h1 and G9a.,Ruan J, Ouyang H, Amaya MF, Ravichandran M, Loppnau P, Min J, Zang J PLoS One. 2012;7(4):e35376. doi: 10.1371/journal.pone.0035376. Epub 2012 Apr 13. PMID:22514736<ref>PMID:22514736</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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==About this Structure==
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</div>
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[[3dm1]] is a 8 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=3DM1 OCA].
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<div class="pdbe-citations 3dm1" style="background-color:#fffaf0;"></div>
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[[Category: Homo sapiens]]
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== References ==
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[[Category: Amaya, M F.]]
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<references/>
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[[Category: Arrowsmith, C H.]]
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__TOC__
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[[Category: Bochkarev, A.]]
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</StructureSection>
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[[Category: Bountra, C.]]
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[[Category: Human]]
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[[Category: Edwards, A M.]]
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[[Category: Large Structures]]
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[[Category: Kozieradzki, I.]]
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[[Category: Amaya, M F]]
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[[Category: Loppnau, P.]]
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[[Category: Arrowsmith, C H]]
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[[Category: Min, J.]]
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[[Category: Bochkarev, A]]
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[[Category: Ouyang, H.]]
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[[Category: Bountra, C]]
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[[Category: Ravichandran, M.]]
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[[Category: Edwards, A M]]
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[[Category: SGC, Structural Genomics Consortium.]]
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[[Category: Kozieradzki, I]]
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[[Category: Weigelt, J.]]
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[[Category: Loppnau, P]]
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[[Category: Min, J]]
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[[Category: Ouyang, H]]
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[[Category: Ravichandran, M]]
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[[Category: Structural genomic]]
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[[Category: Weigelt, J]]
[[Category: Chromatin regulator]]
[[Category: Chromatin regulator]]
[[Category: Chromobox homolog 3]]
[[Category: Chromobox homolog 3]]
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[[Category: Repressor]]
[[Category: Repressor]]
[[Category: Sgc]]
[[Category: Sgc]]
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[[Category: Structural genomic]]
 
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[[Category: Structural genomics consortium]]
 
[[Category: Transcription]]
[[Category: Transcription]]
[[Category: Transcription regulation]]
[[Category: Transcription regulation]]

Current revision

Crystal structure of the complex of human chromobox homolog 3 (CBX3) with peptide

PDB ID 3dm1

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