1dzf: Difference between revisions

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-[[Image:1dzf.jpg|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_1dzf", 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_1dzf|  PDB=1dzf  |  SCENE=  }}
-'''RPB5 FROM S.CEREVISIAE'''
+==RPB5 from S.cerevisiae==
+<StructureSection load='1dzf' size='340' side='right'caption='[[1dzf]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1dzf]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DZF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DZF FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#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=1dzf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dzf OCA], [https://pdbe.org/1dzf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dzf RCSB], [https://www.ebi.ac.uk/pdbsum/1dzf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dzf ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RPAB1_YEAST RPAB1_YEAST] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, RPB5 is part of the lower jaw surrounding the central large cleft and thought to grab the incoming DNA template. Seems to be the major component in this process (By similarity).
+== 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/dz/1dzf_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=1dzf ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Eukaryotic nuclei contain three different types of RNA polymerases (RNAPs), each consisting of 12-18 different subunits. The evolutionarily highly conserved RNAP subunit RPB5 is shared by all three enzymes and therefore represents a key structural/functional component of all eukaryotic RNAPs. Here we present the crystal structure of the RPB5 subunit from Saccharomyces cerevisiae. The bipartite structure includes a eukaryote-specific N-terminal domain and a C-terminal domain resembling the archaeal RNAP subunit H. RPB5 has been implicated in direct protein-protein contacts with transcription factor IIB, one of the components of the RNAP(II) basal transcriptional machinery, and gene-specific activator proteins, such as the hepatitis B virus transactivator protein X. The experimentally mapped regions of RPB5 involved in these interactions correspond to distinct and surface-exposed alpha-helical structures.
-==Overview==
+Crystal structure of RPB5, a universal eukaryotic RNA polymerase subunit and transcription factor interaction target.,Todone F, Weinzierl RO, Brick P, Onesti S Proc Natl Acad Sci U S A. 2000 Jun 6;97(12):6306-10. PMID:10841537<ref>PMID:10841537</ref>
-Eukaryotic nuclei contain three different types of RNA polymerases (RNAPs), each consisting of 12-18 different subunits. The evolutionarily highly conserved RNAP subunit RPB5 is shared by all three enzymes and therefore represents a key structural/functional component of all eukaryotic RNAPs. Here we present the crystal structure of the RPB5 subunit from Saccharomyces cerevisiae. The bipartite structure includes a eukaryote-specific N-terminal domain and a C-terminal domain resembling the archaeal RNAP subunit H. RPB5 has been implicated in direct protein-protein contacts with transcription factor IIB, one of the components of the RNAP(II) basal transcriptional machinery, and gene-specific activator proteins, such as the hepatitis B virus transactivator protein X. The experimentally mapped regions of RPB5 involved in these interactions correspond to distinct and surface-exposed alpha-helical structures.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-DZF is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DZF OCA].
+</div>
+<div class="pdbe-citations 1dzf" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Crystal structure of RPB5, a universal eukaryotic RNA polymerase subunit and transcription factor interaction target., Todone F, Weinzierl RO, Brick P, Onesti S, Proc Natl Acad Sci U S A. 2000 Jun 6;97(12):6306-10. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10841537 10841537]
+*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
-[[Category: DNA-directed RNA polymerase]]
+== References ==
-[[Category: Saccharomyces cerevisiae]]
+<references/>
-[[Category: Single protein]]
+__TOC__
-[[Category: Brick, P.]]
+</StructureSection>
-[[Category: Onesti, S.]]
+[[Category: Large Structures]]
-[[Category: Todone, F.]]
+[[Category: Saccharomyces cerevisiae S288C]]
-[[Category: Weinzierl, R O.J.]]
+[[Category: Brick P]]
-[[Category: Rna polymerase subunit]]
+[[Category: Onesti S]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 14:28:16 2008''
+[[Category: Todone F]]
+[[Category: Weinzierl ROJ]]