2nvy

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{{Seed}}
 
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[[Image:2nvy.png|left|200px]]
 
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==RNA Polymerase II form II in 150 mM Mn+2==
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The line below this paragraph, containing "STRUCTURE_2nvy", creates the "Structure Box" on the page.
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<StructureSection load='2nvy' size='340' side='right'caption='[[2nvy]], [[Resolution|resolution]] 3.40&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'>[[2nvy]] 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=2NVY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2NVY 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]] 3.4&#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=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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{{STRUCTURE_2nvy| PDB=2nvy | 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=2nvy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2nvy OCA], [https://pdbe.org/2nvy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2nvy RCSB], [https://www.ebi.ac.uk/pdbsum/2nvy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2nvy ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/RPB2_YEAST RPB2_YEAST] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Second largest component of RNA polymerases II which synthesizes mRNA precursors and many functional non-coding RNAs. Proposed to contribute to the polymerase catalytic activity and forms the polymerase active center together with the largest subunit. Pol II is the central component of the basal RNA polymerase II transcription machinery. During a transcription cycle, Pol II, general transcription factors and the Mediator complex assemble as the preinitiation complex (PIC) at the promoter. 11-15 base pairs of DNA surrounding the transcription start site are melted and the single stranded DNA template strand of the promoter is positioned deeply within the central active site cleft of Pol II to form the open complex. After synthesis of about 30 bases of RNA, Pol II releases its contacts with the core promoter and the rest of the transcription machinery (promoter clearance) and enters the stage of transcription elongation in which it moves on the template as the transcript elongates. Pol II appears to oscillate between inactive and active conformations at each step of nucleotide addition. Pol II is composed of mobile elements that move relative to each other. The core element with the central large cleft comprises RPB3, RBP10, RPB11, RPB12 and regions of RPB1 and RPB2 forming the active center. The clamp element (portions of RPB1, RPB2 and RPB3) is connected to the core through a set of flexible switches and moves to open and close the cleft. The cleft is surrounded by jaws: an upper jaw formed by portions of RBP1, RPB2 and RPB9, and a lower jaw. The jaws are thought to grab the incoming DNA template. The fork loop 1 (RPB2) interacts with the RNA-DNA hybrid, possibly stabilizing it.
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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/2nvy_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=2nvy ConSurf].
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<div style="clear:both"></div>
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===RNA Polymerase II form II in 150 mM Mn+2===
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==See Also==
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*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
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__TOC__
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</StructureSection>
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The line below this paragraph, {{ABSTRACT_PUBMED_17129781}}, adds the Publication Abstract to the page
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[[Category: Large 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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{{ABSTRACT_PUBMED_17129781}}
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==About this Structure==
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2NVY is a [[Protein complex]] 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=2NVY OCA].
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==Reference==
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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:[http://www.ncbi.nlm.nih.gov/pubmed/17129781 17129781]
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[[Category: DNA-directed RNA polymerase]]
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[[Category: Protein complex]]
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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: Kaplan, C D.]]
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[[Category: Kaplan CD]]
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[[Category: Kornberg, R D.]]
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[[Category: Kornberg RD]]
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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: Dna]]
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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 Jul 29 03:12:06 2008''
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Current revision

RNA Polymerase II form II in 150 mM Mn+2

PDB ID 2nvy

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