1aay: Difference between revisions

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-{{Seed}}
-[[Image:1aay.png|left|200px]]
-<!--
+==ZIF268 ZINC FINGER-DNA COMPLEX==
-The line below this paragraph, containing "STRUCTURE_1aay", creates the "Structure Box" on the page.
+<StructureSection load='1aay' size='340' side='right'caption='[[1aay]], [[Resolution|resolution]] 1.60&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'>[[1aay]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AAY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1AAY 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]] 1.6&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-{{STRUCTURE_1aay|  PDB=1aay  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1aay FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1aay OCA], [https://pdbe.org/1aay PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1aay RCSB], [https://www.ebi.ac.uk/pdbsum/1aay PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1aay ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/EGR1_MOUSE EGR1_MOUSE] Transcriptional regulator. Recognizes and binds to the DNA sequence 5'-CGCCCCCGC-3'(EGR-site). Activates the transcription of target genes whose products are required for mitogenesis and differentiation.
+== 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/aa/1aay_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=1aay ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+BACKGROUND: Zinc fingers of the Cys2 His2 class recognize a wide variety of different DNA sequences and are one of the most abundant DNA-binding motifs found in eukaryotes. The previously determined 2.1 A structure of a complex containing the three zinc fingers from Zif268 has served as a basis for many modeling and design studies, and Zif268 has proved to be a very useful model system for studying how TFIIIA-like zinc fingers recognize DNA. RESULTS: We have refined the structure of the Zif268 protein-DNA complex at 1.6 A resolution. Our structure confirms all the basic features of the previous model and allows us to focus on some critical details at the protein-DNA interface. In particular, our refined structure helps explain the roles of several acidic residues located in the recognition helices and shows that the zinc fingers make a number of water-mediated contacts with bases and phosphates. Modeling studies suggest that the distinctive DNA conformation observed in the Zif268-DNA complex is correlated with finger-finger interactions and the length of the linkers between adjacent fingers. Circular dichroism studies indicate that at least some of the features of this distinctive DNA conformation are induced upon complex formation. CONCLUSIONS: Our 1.6 A structure should provide an excellent framework for analyzing the effects of Zif268 mutations, for modeling related zinc finger-DNA complexes, and for designing and selecting Zif268 variants that will recognize other DNA sites.
-===ZIF268 ZINC FINGER-DNA COMPLEX===
+Zif268 protein-DNA complex refined at 1.6 A: a model system for understanding zinc finger-DNA interactions.,Elrod-Erickson M, Rould MA, Nekludova L, Pabo CO Structure. 1996 Oct 15;4(10):1171-80. PMID:8939742<ref>PMID:8939742</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_8939742}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1aay" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 8939742 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_8939742}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-AAY is a 3 chains structure of sequences from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AAY OCA].
-==Reference==
-<ref group="xtra">PMID:8939742</ref><references group="xtra"/>
 [[Category: Mus musculus]]
-[[Category: Elrod-Erickson, M.]]
+[[Category: Elrod-Erickson M]]
-[[Category: Pabo, C O.]]
+[[Category: Pabo CO]]
-[[Category: Rould, M A.]]
+[[Category: Rould MA]]
-[[Category: Dna-binding protein]]
-[[Category: Zinc finger]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 06:57:01 2009''