1y77

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[[Image:1y77.png|left|200px]]
 
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==Complete RNA Polymerase II elongation complex with substrate analogue GMPCPP==
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The line below this paragraph, containing "STRUCTURE_1y77", creates the "Structure Box" on the page.
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<StructureSection load='1y77' size='340' side='right'caption='[[1y77]], [[Resolution|resolution]] 4.50&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'>[[1y77]] 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=1Y77 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Y77 FirstGlance]. <br>
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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]] 4.5&#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=G2P:PHOSPHOMETHYLPHOSPHONIC+ACID+GUANYLATE+ESTER'>G2P</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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{{STRUCTURE_1y77| PDB=1y77 | 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=1y77 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1y77 OCA], [https://pdbe.org/1y77 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1y77 RCSB], [https://www.ebi.ac.uk/pdbsum/1y77 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1y77 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/RPAB4_YEAST RPAB4_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 a small RNAs, such as 5S rRNA and tRNAs, respectively. Pols are composed of mobile elements that move relative to each other. In Pol II, the core element with the central large cleft comprises RPB3, RBP10, RPB11, RPB12 and regions of RPB1 and RPB2 forming the active center.
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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/y7/1y77_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=1y77 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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The crystal structure of the complete 12 subunit RNA polymerase (pol) II bound to a transcription bubble and product RNA reveals incoming template and nontemplate DNA, a seven base pair DNA/RNA hybrid, and three nucleotides each of separating DNA and RNA. The complex adopts the posttranslocation state and accommodates a cocrystallized nucleoside triphosphate (NTP) substrate. The NTP binds in the active site pore at a position to interact with a DNA template base. Residues surrounding the NTP are conserved in all cellular RNA polymerases, suggesting a universal mechanism of NTP selection and incorporation. DNA-DNA and DNA-RNA strand separation may be explained by pol II-induced duplex distortions. Four protein loops partition the active center cleft, contribute to embedding the hybrid, prevent strand reassociation, and create an RNA exit tunnel. Binding of the elongation factor TFIIS realigns RNA in the active center, possibly converting the elongation complex to an alternative state less prone to stalling.
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===Complete RNA Polymerase II elongation complex with substrate analogue GMPCPP===
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Complete RNA polymerase II elongation complex structure and its interactions with NTP and TFIIS.,Kettenberger H, Armache KJ, Cramer P Mol Cell. 2004 Dec 22;16(6):955-65. PMID:15610738<ref>PMID:15610738</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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The line below this paragraph, {{ABSTRACT_PUBMED_15610738}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 1y77" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 15610738 is the PubMed ID number.
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{{ABSTRACT_PUBMED_15610738}}
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==About this Structure==
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[[1y77]] is a 15 chain structure of [[RNA polymerase]] with 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=1Y77 OCA].
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==See Also==
==See Also==
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*[[RNA polymerase]]
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*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
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== References ==
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==Reference==
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<references/>
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<ref group="xtra">PMID:015610738</ref><references group="xtra"/>
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__TOC__
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[[Category: DNA-directed RNA polymerase]]
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</StructureSection>
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[[Category: Large Structures]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Saccharomyces cerevisiae]]
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[[Category: Armache, K J.]]
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[[Category: Armache K-J]]
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[[Category: Cramer, P.]]
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[[Category: Cramer P]]
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[[Category: Kettenberger, H.]]
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[[Category: Kettenberger H]]
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[[Category: Elongation]]
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[[Category: Ntp]]
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[[Category: Substrate]]
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[[Category: Transcription]]
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[[Category: Transferase-dna-rna hybrid complex]]
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Current revision

Complete RNA Polymerase II elongation complex with substrate analogue GMPCPP

PDB ID 1y77

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Proteopedia Page Contributors and Editors (what is this?)

OCA

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