3s1n

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==RNA Polymerase II Initiation Complex with a 5-nt RNA (variant 2)==
==RNA Polymerase II Initiation Complex with a 5-nt RNA (variant 2)==
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<StructureSection load='3s1n' size='340' side='right' caption='[[3s1n]], [[Resolution|resolution]] 3.10&Aring;' scene=''>
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<StructureSection load='3s1n' size='340' side='right'caption='[[3s1n]], [[Resolution|resolution]] 3.10&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3s1n]] is a 12 chain structure 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=3S1N OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3S1N FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3s1n]] 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=3S1N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3S1N FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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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]] 3.1&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3s1m|3s1m]], [[3rzo|3rzo]], [[3s1q|3s1q]], [[3s1r|3s1r]], [[3s2d|3s2d]], [[3s2h|3s2h]], [[3rzd|3rzd]], [[3s14|3s14]], [[3s15|3s15]], [[3s16|3s16]], [[3s17|3s17]]</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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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA-directed_RNA_polymerase DNA-directed RNA polymerase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.7.6 2.7.7.6] </span></td></tr>
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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=3s1n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s1n OCA], [https://pdbe.org/3s1n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3s1n RCSB], [https://www.ebi.ac.uk/pdbsum/3s1n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3s1n ProSAT]</span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3s1n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s1n OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3s1n RCSB], [http://www.ebi.ac.uk/pdbsum/3s1n PDBsum]</span></td></tr>
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</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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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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The initiation of transcription by RNA polymerase II is a multistage process. X-ray crystal structures of transcription complexes containing short RNAs reveal three structural states: one with 2- and 3-nucleotide RNAs, in which only the 3'-end of the RNA is detectable; a second state with 4- and 5-nucleotide RNAs, with an RNA-DNA hybrid in a grossly distorted conformation; and a third state with RNAs of 6 nucleotides and longer, essentially the same as a stable elongating complex. The transition from the first to the second state correlates with a markedly reduced frequency of abortive initiation. The transition from the second to the third state correlates with partial "bubble collapse" and promoter escape. Polymerase structure is permissive for abortive initiation, thereby setting a lower limit on polymerase-promoter complex lifetime and allowing the dissociation of nonspecific complexes. Abortive initiation may be viewed as promoter proofreading, and the structural transitions as checkpoints for promoter control.
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Initiation complex structure and promoter proofreading.,Liu X, Bushnell DA, Silva DA, Huang X, Kornberg RD Science. 2011 Jul 29;333(6042):633-7. PMID:21798951<ref>PMID:21798951</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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==See Also==
==See Also==
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*[[RNA polymerase|RNA polymerase]]
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*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: DNA-directed RNA polymerase]]
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[[Category: Large Structures]]
[[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: Liu, X]]
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[[Category: Liu X]]
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[[Category: Silva, D A]]
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[[Category: Silva DA]]
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[[Category: Initiation complex]]
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[[Category: Rna polymerase ii]]
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[[Category: Transcription-rna-dna complex]]
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Current revision

RNA Polymerase II Initiation Complex with a 5-nt RNA (variant 2)

PDB ID 3s1n

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