2nvz

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{{Seed}}
 
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[[Image:2nvz.png|left|200px]]
 
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==RNA Polymerase II elongation complex with UTP, updated 11/2006==
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The line below this paragraph, containing "STRUCTURE_2nvz", creates the "Structure Box" on the page.
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<StructureSection load='2nvz' size='340' side='right'caption='[[2nvz]], [[Resolution|resolution]] 4.30&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'>[[2nvz]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2NVZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2NVZ 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]] 4.3&#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=UTP:URIDINE+5-TRIPHOSPHATE'>UTP</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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{{STRUCTURE_2nvz| PDB=2nvz | 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=2nvz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nvz OCA], [https://pdbe.org/2nvz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2nvz RCSB], [https://www.ebi.ac.uk/pdbsum/2nvz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2nvz ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/RPB3_YEAST RPB3_YEAST] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase II which synthesizes mRNA precursors and many functional non-coding RNAs. Pol II is the central component of the basal RNA polymerase II transcription machinery. It is composed of mobile elements that move relative to each other. RPB3 is part of the core element with the central large cleft and the clamp element that moves to open and close the cleft. Seems to be involved in transcription termination.
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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/nv/2nvz_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=2nvz 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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New structures of RNA polymerase II (pol II) transcribing complexes reveal a likely key to transcription. The trigger loop swings beneath a correct nucleoside triphosphate (NTP) in the nucleotide addition site, closing off the active center and forming an extensive network of interactions with the NTP base, sugar, phosphates, and additional pol II residues. A histidine side chain in the trigger loop, precisely positioned by these interactions, may literally "trigger" phosphodiester bond formation. Recognition and catalysis are thus coupled, ensuring the fidelity of transcription.
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===RNA Polymerase II elongation complex with UTP, updated 11/2006===
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Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis.,Wang D, Bushnell DA, Westover KD, Kaplan CD, Kornberg RD Cell. 2006 Dec 1;127(5):941-54. PMID:17129781<ref>PMID:17129781</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 2nvz" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_17129781}}, 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 17129781 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_17129781}}
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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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2NVZ 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=2NVZ OCA].
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==Reference==
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<ref group="xtra">PMID:17129781</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: Synthetic construct]]
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[[Category: Kaplan, C D.]]
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[[Category: Bushnell DA]]
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[[Category: Kornberg, R D.]]
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[[Category: Kaplan CD]]
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[[Category: Wang, D.]]
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[[Category: Kornberg RD]]
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[[Category: Westover, K D.]]
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[[Category: Wang D]]
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[[Category: Dna]]
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[[Category: Westover KD]]
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[[Category: Molecular machine]]
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[[Category: Mrna]]
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[[Category: Multiprotein complex]]
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[[Category: Transcription]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 00:34:32 2009''
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Current revision

RNA Polymerase II elongation complex with UTP, updated 11/2006

PDB ID 2nvz

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