3s14: Difference between revisions

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==RNA Polymerase II Initiation Complex with a 6-nt RNA==
==RNA Polymerase II Initiation Complex with a 6-nt RNA==
<StructureSection load='3s14' size='340' side='right' caption='[[3s14]], [[Resolution|resolution]] 2.85&Aring;' scene=''>
<StructureSection load='3s14' size='340' side='right'caption='[[3s14]], [[Resolution|resolution]] 2.85&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3s14]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_s288c Saccharomyces cerevisiae s288c]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S14 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3S14 FirstGlance]. <br>
<table><tr><td colspan='2'>[[3s14]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3S14 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3S14 FirstGlance]. <br>
</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>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.85&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3rzo|3rzo]], [[3rzd|3rzd]], [[3s15|3s15]], [[3s16|3s16]], [[3s17|3s17]], [[3s1m|3s1m]], [[3s1n|3s1n]], [[3s1q|3s1q]], [[3s1r|3s1r]], [[3s2d|3s2d]], [[3s2h|3s2h]]</td></tr>
<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>
<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>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3s14 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s14 OCA], [https://pdbe.org/3s14 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3s14 RCSB], [https://www.ebi.ac.uk/pdbsum/3s14 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3s14 ProSAT]</span></td></tr>
<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=3s14 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s14 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3s14 RCSB], [http://www.ebi.ac.uk/pdbsum/3s14 PDBsum]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Function ==
== Publication Abstract from PubMed ==
[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.
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.
 
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>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
 
==See Also==
*[[RNA polymerase|RNA polymerase]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: DNA-directed RNA polymerase]]
[[Category: Large Structures]]
[[Category: Saccharomyces cerevisiae s288c]]
[[Category: Saccharomyces cerevisiae S288C]]
[[Category: Bushnell, D A]]
[[Category: Bushnell DA]]
[[Category: Huang, X]]
[[Category: Huang X]]
[[Category: Kornberg, R D]]
[[Category: Kornberg RD]]
[[Category: Liu, X]]
[[Category: Liu X]]
[[Category: Silva, D A]]
[[Category: Silva DA]]
[[Category: Initiation complex]]
[[Category: Rna polymerase ii]]
[[Category: Transcription-rna-dna complex]]

Latest revision as of 15:42, 14 March 2024

RNA Polymerase II Initiation Complex with a 6-nt RNARNA Polymerase II Initiation Complex with a 6-nt RNA

Structural highlights

3s14 is a 10 chain structure with sequence from Saccharomyces cerevisiae S288C. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.85Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.

3s14, resolution 2.85Å

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