3nm9: Difference between revisions

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-{{Seed}}
-[[Image:3nm9.png|left|200px]]
-<!--
+==HMGD(M13A)-DNA complex==
-The line below this paragraph, containing "STRUCTURE_3nm9", creates the "Structure Box" on the page.
+<StructureSection load='3nm9' size='340' side='right'caption='[[3nm9]], [[Resolution|resolution]] 2.85&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'>[[3nm9]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NM9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3NM9 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]] 2.85&#8491;</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=3nm9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3nm9 OCA], [https://pdbe.org/3nm9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3nm9 RCSB], [https://www.ebi.ac.uk/pdbsum/3nm9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3nm9 ProSAT]</span></td></tr>
-{{STRUCTURE_3nm9|  PDB=3nm9  |  SCENE=  }}
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/HMGD_DROME HMGD_DROME] Binds preferentially single-stranded DNA and unwinds double stranded DNA. Prefers sites containing the sequence 5'-ttg-3'. Facilitates DNA bending. Associated with early embryonic chromatin in the absence of histone H1.<ref>PMID:1373803</ref> <ref>PMID:8168480</ref> <ref>PMID:7720717</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/nm/3nm9_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=3nm9 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The ubiquitous, eukaryotic, high-mobility group box (HMGB) chromosomal proteins promote many chromatin-mediated cellular activities through their non-sequence-specific binding and bending of DNA. Minor-groove DNA binding by the HMG box results in substantial DNA bending toward the major groove owing to electrostatic interactions, shape complementarity, and DNA intercalation that occurs at two sites. Here, the structures of the complexes formed with DNA by a partially DNA intercalation-deficient mutant of Drosophila melanogaster HMGD have been determined by X-ray crystallography at a resolution of 2.85 A. The six proteins and 50 bp of DNA in the crystal structure revealed a variety of bound conformations. All of the proteins bound in the minor groove, bridging DNA molecules, presumably because these DNA regions are easily deformed. The loss of the primary site of DNA intercalation decreased overall DNA bending and shape complementarity. However, DNA bending at the secondary site of intercalation was retained and most protein-DNA contacts were preserved. The mode of binding resembles the HMGB1 box A-cisplatin-DNA complex, which also lacks a primary intercalating residue. This study provides new insights into the binding mechanisms used by HMG boxes to recognize varied DNA structures and sequences as well as modulate DNA structure and DNA bending.
-===HMGD(M13A)-DNA complex===
+Structural Analysis of HMGD-DNA Complexes Reveals Influence of Intercalation on Sequence Selectivity and DNA Bending.,Churchill ME, Klass J, Zoetewey DL J Mol Biol. 2010 Aug 25. PMID:20800069<ref>PMID:20800069</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3nm9" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_20800069}}, adds the Publication Abstract to the page
+*[[High mobility group protein|High mobility group protein]]
-(as it appears on PubMed at http://www.pubmed.gov), where 20800069 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_20800069}}
+__TOC__
+</StructureSection>
-==About this Structure==
-NM9 is a 16 chains structure with sequences from [http://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NM9 OCA].
-==Reference==
-<ref group="xtra">PMID:20800069</ref><references group="xtra"/>
 [[Category: Drosophila melanogaster]]
-[[Category: Churchill, M E.A.]]
+[[Category: Large Structures]]
-[[Category: Klass, J.]]
+[[Category: Churchill MEA]]
-[[Category: Zoetewey, D L.]]
+[[Category: Klass J]]
-[[Category: Chromosomal protein]]
+[[Category: Zoetewey DL]]
-[[Category: Dna]]
-[[Category: Dna bending]]
-[[Category: Gene regulation-dna complex]]
-[[Category: High mobility group]]
-[[Category: Hmg domain]]
-[[Category: Non-sequence-specific]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Dec  8 11:16:31 2010''