1e7j: Difference between revisions

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-{{Seed}}
-[[Image:1e7j.png|left|200px]]
-<!--
+==HMG-D complexed to a bulge DNA==
-The line below this paragraph, containing "STRUCTURE_1e7j", creates the "Structure Box" on the page.
+<StructureSection load='1e7j' size='340' side='right'caption='[[1e7j]]' 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'>[[1e7j]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1E7J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1E7J 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">Solution NMR</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=1e7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1e7j OCA], [https://pdbe.org/1e7j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1e7j RCSB], [https://www.ebi.ac.uk/pdbsum/1e7j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1e7j ProSAT]</span></td></tr>
-{{STRUCTURE_1e7j|  PDB=1e7j  |  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/e7/1e7j_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=1e7j ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+An NMR model is presented for the structure of HMG-D, one of the DROSOPHILA: counterparts of mammalian HMG1/2 proteins, bound to a particular distorted DNA structure, a dA(2) DNA bulge. The complex is in fast to intermediate exchange on the NMR chemical shift time scale and suffers substantial linebroadening for the majority of interfacial resonances. This essentially precludes determination of a high-resolution structure for the interface based on NMR data alone. However, by introducing a small number of additional constraints based on chemical shift and linewidth footprinting combined with analogies to known structures, an ensemble of model structures was generated using a computational strategy equivalent to that for a conventional NMR structure determination. We find that the base pair adjacent to the dA(2) bulge is not formed and that the protein recognizes this feature in forming the complex; intermolecular NOE enhancements are observed from the sidechain of Thr 33 to all four nucleotides of the DNA sequence step adjacent to the bulge. Our results form the first experimental demonstration that when binding to deformed DNA, non-sequence-specific HMG proteins recognize the junction between duplex and nonduplex DNA. Similarities and differences of the present structural model relative to other HMG-DNA complex structures are discussed.
-===HMG-D COMPLEXED TO A BULGE DNA===
+HMG-D complexed to a bulge DNA: an NMR model.,Cerdan R, Payet D, Yang JC, Travers AA, Neuhaus D Protein Sci. 2001 Mar;10(3):504-18. PMID:11344319<ref>PMID:11344319</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1e7j" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_11344319}}, 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 11344319 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_11344319}}
+__TOC__
+</StructureSection>
-==About this Structure==
-E7J is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Drosophila_melanogaster Drosophila melanogaster]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1E7J OCA].
-==Reference==
-HMG-D complexed to a bulge DNA: an NMR model., Cerdan R, Payet D, Yang JC, Travers AA, Neuhaus D, Protein Sci. 2001 Mar;10(3):504-18. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11344319 11344319]
 [[Category: Drosophila melanogaster]]
-[[Category: Protein complex]]
+[[Category: Large Structures]]
-[[Category: Cerdan, R.]]
+[[Category: Cerdan R]]
-[[Category: Neuhaus, D.]]
+[[Category: Neuhaus D]]
-[[Category: Payet, D.]]
+[[Category: Payet D]]
-[[Category: Travers, A.]]
+[[Category: Travers AA]]
-[[Category: Yang, J C.]]
+[[Category: Yang J-C]]
-[[Category: Protein-dna complex]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul  1 00:16:54 2008''