3afa: Difference between revisions

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-{{Seed}}
-[[Image:3afa.png|left|200px]]
-<!--
+==The human nucleosome structure==
-The line below this paragraph, containing "STRUCTURE_3afa", creates the "Structure Box" on the page.
+<StructureSection load='3afa' size='340' side='right'caption='[[3afa]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[3afa]] is a 10 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=3AFA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3AFA FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</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=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
-{{STRUCTURE_3afa|  PDB=3afa  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3afa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3afa OCA], [https://pdbe.org/3afa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3afa RCSB], [https://www.ebi.ac.uk/pdbsum/3afa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3afa ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/H31_HUMAN H31_HUMAN]
+== 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/af/3afa_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/main_output.php?pdb_ID=3afa ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+A histone H3 variant, H3T, is highly expressed in the testis, suggesting that it may play an important role in the chromatin reorganization required for meiosis and/or spermatogenesis. In the present study, we found that the nucleosome containing human H3T is significantly unstable both in vitro and in vivo, as compared to the conventional nucleosome containing H3.1. The crystal structure of the H3T nucleosome revealed structural differences in the H3T regions on both ends of the central alpha2 helix, as compared to those of H3.1. The H3T-specific residues (Met71 and Val111) are the source of the structural differences observed between H3T and H3.1. A mutational analysis revealed that these residues are responsible for the reduced stability of the H3T-containing nucleosome. These physical and structural properties of the H3T-containing nucleosome may provide the basis of chromatin reorganization during spermatogenesis.
-===The human nucleosome structure===
+Structural basis of instability of the nucleosome containing a testis-specific histone variant, human H3T.,Tachiwana H, Kagawa W, Osakabe A, Kawaguchi K, Shiga T, Hayashi-Takanaka Y, Kimura H, Kurumizaka H Proc Natl Acad Sci U S A. 2010 Jun 8;107(23):10454-9. Epub 2010 May 24. PMID:20498094<ref>PMID:20498094</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3afa" style="background-color:#fffaf0;"></div>
-==About this Structure==
+==See Also==
-AFA is a 10 chains structure with sequences 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=3AFA OCA].
+*[[Histone 3D structures|Histone 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Kagawa, W.]]
+[[Category: Large Structures]]
-[[Category: Kimura, H.]]
+[[Category: Kagawa W]]
-[[Category: Koichiro, K.]]
+[[Category: Kimura H]]
-[[Category: Kurumizaka, H.]]
+[[Category: Koichiro K]]
-[[Category: Osakabe, A.]]
+[[Category: Kurumizaka H]]
-[[Category: Shiga, T.]]
+[[Category: Osakabe A]]
-[[Category: Tachiwana, H.]]
+[[Category: Shiga T]]
-[[Category: Acetylation]]
+[[Category: Tachiwana H]]
-[[Category: Antibiotic]]
-[[Category: Antimicrobial]]
-[[Category: Chromosomal protein]]
-[[Category: Citrullination]]
-[[Category: Dna-binding]]
-[[Category: Dna-binding protein]]
-[[Category: Histone-fold]]
-[[Category: Isopeptide bond]]
-[[Category: Methylation]]
-[[Category: Nucleosome core]]
-[[Category: Nucleus]]
-[[Category: Phosphoprotein]]
-[[Category: Polymorphism]]
-[[Category: Structural protein-dna complex]]
-[[Category: Ubl conjugation]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jun  2 08:24:25 2010''