3gto

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{{Seed}}
 
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[[Image:3gto.jpg|left|200px]]
 
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==Backtracked RNA polymerase II complex with 15mer RNA==
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The line below this paragraph, containing "STRUCTURE_3gto", creates the "Structure Box" on the page.
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<StructureSection load='3gto' size='340' side='right'caption='[[3gto]], [[Resolution|resolution]] 4.00&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[3gto]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3GTO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3GTO FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 4&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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{{STRUCTURE_3gto| PDB=3gto | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3gto FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3gto OCA], [https://pdbe.org/3gto PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3gto RCSB], [https://www.ebi.ac.uk/pdbsum/3gto PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3gto ProSAT]</span></td></tr>
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</table>
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== Function ==
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[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).
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gt/3gto_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=3gto ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Transcribing RNA polymerases oscillate between three stable states, two of which, pre- and posttranslocated, were previously subjected to x-ray crystal structure determination. We report here the crystal structure of RNA polymerase II in the third state, the reverse translocated, or "backtracked" state. The defining feature of the backtracked structure is a binding site for the first backtracked nucleotide. This binding site is occupied in case of nucleotide misincorporation in the RNA or damage to the DNA, and is termed the "P" site because it supports proofreading. The predominant mechanism of proofreading is the excision of a dinucleotide in the presence of the elongation factor SII (TFIIS). Structure determination of a cocrystal with TFIIS reveals a rearrangement whereby cleavage of the RNA may take place.
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===Backtracked RNA polymerase II complex with 15mer RNA===
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Structural basis of transcription: backtracked RNA polymerase II at 3.4 angstrom resolution.,Wang D, Bushnell DA, Huang X, Westover KD, Levitt M, Kornberg RD Science. 2009 May 29;324(5931):1203-6. PMID:19478184<ref>PMID:19478184</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3gto" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_19478184}}, adds the Publication Abstract to the page
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*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 19478184 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_19478184}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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3GTO is a 13 chains structure of sequences 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=3GTO OCA].
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==Reference==
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<ref group="xtra">PMID:19478184</ref><references group="xtra"/>
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[[Category: DNA-directed RNA polymerase]]
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[[Category: Saccharomyces cerevisiae]]
[[Category: Saccharomyces cerevisiae]]
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[[Category: Bushnell, D A.]]
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[[Category: Bushnell DA]]
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[[Category: Huang, X.]]
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[[Category: Huang X]]
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[[Category: Kornberg, R D.]]
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[[Category: Kornberg RD]]
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[[Category: Levitt, M.]]
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[[Category: Levitt M]]
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[[Category: Wang, D.]]
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[[Category: Wang D]]
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[[Category: Westover, K D.]]
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[[Category: Westover KD]]
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[[Category: Backtrack]]
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[[Category: Cytoplasm]]
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[[Category: Dna binding]]
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[[Category: Dna damage]]
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[[Category: Dna repair]]
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[[Category: Dna-directed rna polymerase]]
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[[Category: Dna-rna hybrid]]
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[[Category: Isopeptide bond]]
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[[Category: Magnesium]]
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[[Category: Metal binding]]
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[[Category: Nucleotidyltransferase]]
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[[Category: Nucleus]]
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[[Category: Phosphoprotein]]
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[[Category: Polymorphism]]
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[[Category: Transcription]]
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[[Category: Transferase]]
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[[Category: Transferase/dna-rna hybrid complex]]
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[[Category: Ubl conjugation]]
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[[Category: Zinc]]
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[[Category: Zinc-finger]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jun 10 18:06:59 2009''
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Current revision

Backtracked RNA polymerase II complex with 15mer RNA

PDB ID 3gto

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Proteopedia Page Contributors and Editors (what is this?)

OCA

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