Ann Taylor sandbox 3: Difference between revisions

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Ann Taylor, Austin Childress

@@ Line 1: / Line 1: @@
-{{Seed}}
+==DNA RECOGNITION BY GAL4: STRUCTURE OF A PROTEIN/DNA COMPLEX==
-[[Image:3d06.jpg|left|200px]]
+<StructureSection load='1d66' size='340' side='right'caption='[[1d66]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1d66]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D66 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D66 FirstGlance]. <br>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CD:CADMIUM+ION'>CD</scene></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=1d66 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d66 OCA], [https://pdbe.org/1d66 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d66 RCSB], [https://www.ebi.ac.uk/pdbsum/1d66 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d66 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[[https://www.uniprot.org/uniprot/GAL4_YEAST GAL4_YEAST]] This protein is a positive regulator for the gene expression of the galactose-induced genes such as GAL1, GAL2, GAL7, GAL10, and MEL1 which code for the enzymes used to convert galactose to glucose. It recognizes a 17 base pair sequence in (5'-CGGRNNRCYNYNCNCCG-3') the upstream activating sequence (UAS-G) of these genes.
+== 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/d6/1d66_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=1d66 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+A specific DNA complex of the 65-residue, N-terminal fragment of the yeast transcriptional activator, GAL4, has been analysed at 2.7 A resolution by X-ray crystallography. The protein binds as a dimer to a symmetrical 17-base-pair sequence. A small, Zn(2+)-containing domain recognizes a conserved CCG triplet at each end of the site through direct contacts with the major groove. A short coiled-coil dimerization element imposes 2-fold symmetry. A segment of extended polypeptide chain links the metal-binding module to the dimerization element and specifies the length of the site. The relatively open structure of the complex would allow another protein to bind coordinately with GAL4.
+Gal4 has lots of <scene name='89/891376/Basic_aas/2'>basic amino acids</scene> that interact with DNA.
-<!--
+DNA recognition by GAL4: structure of a protein-DNA complex.,Marmorstein R, Carey M, Ptashne M, Harrison SC Nature. 1992 Apr 2;356(6368):408-14. PMID:1557122<ref>PMID:1557122</ref>
-The line below this paragraph, containing "STRUCTURE_3d06", creates the "Structure Box" on the page.
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-or leave the SCENE parameter empty for the default display.
--->
-{{STRUCTURE_3d06|  PDB=3d06  |  SCENE=  }}
-===Human p53 core domain with hot spot mutation R249S (I)===
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1d66" style="background-color:#fffaf0;"></div>
+==See Also==
-<!--
+*[[Gal3-Gal80-Gal4|Gal3-Gal80-Gal4]]
-The line below this paragraph, {{ABSTRACT_PUBMED_18996393}}, adds the Publication Abstract to the page
+*[[Hydrogen in macromolecular models|Hydrogen in macromolecular models]]
-(as it appears on PubMed at http://www.pubmed.gov), where 18996393 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_18996393}}
+__TOC__
+</StructureSection>
-==Disease==
+[[Category: Atcc 18824]]
-Known disease associated with this structure: Adrenal cortical carcinoma OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=191170 191170]], Breast cancer OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=191170 191170]], Colorectal cancer OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=191170 191170]], Hepatocellular carcinoma OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=191170 191170]], Histiocytoma OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=191170 191170]], Li-Fraumeni syndrome OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=191170 191170]], Multiple malignancy syndrome OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=191170 191170]], Nasopharyngeal carcinoma OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=191170 191170]], Osteosarcoma OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=191170 191170]], Pancreatic cancer OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=191170 191170]], Thyroid carcinoma OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=191170 191170]]
+[[Category: Large Structures]]
+[[Category: Carey, M]]
-==About this Structure==
+[[Category: Harrison, S C]]
-D06 is a 1 chain structure of 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=3D06 OCA].
+[[Category: Marmorstein, R]]
+[[Category: Ptashne, M]]
-==Reference==
+[[Category: Double helix]]
-<ref group="xtra">PMID:18996393</ref><references group="xtra"/>
+[[Category: Protein-dna complex]]
-[[Category: Homo sapiens]]
+[[Category: Transcription-dna complex]]
-[[Category: Frolow, F.]]
-[[Category: Rozenberg, H.]]
-[[Category: Shakked, Z.]]
-[[Category: Shimon, L J.W.]]
-[[Category: Suad, O.]]
-[[Category: Acetylation]]
-[[Category: Activator]]
-[[Category: Alternative splicing]]
-[[Category: Anti-oncogene]]
-[[Category: Apoptosis]]
-[[Category: Cell cycle]]
-[[Category: Covalent protein-rna linkage]]
-[[Category: Cytoplasm]]
-[[Category: Disease mutation]]
-[[Category: Dna-binding]]
-[[Category: Endoplasmic reticulum]]
-[[Category: Glycoprotein]]
-[[Category: Host-virus interaction]]
-[[Category: Li-fraumeni syndrome]]
-[[Category: Loop-sheet-helix motif]]
-[[Category: Metal-binding]]
-[[Category: Methylation]]
-[[Category: Mutant protein]]
-[[Category: Nucleus]]
-[[Category: P53]]
-[[Category: Phosphoprotein]]
-[[Category: Polymorphism]]
-[[Category: Transcription]]
-[[Category: Transcription regulation]]
-[[Category: Ubl conjugation]]
-[[Category: Zinc]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 21 10:44:12 2009''