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| ==RNA Polymerase I Closed Conformation 2 (CC2)== | | ==RNA Polymerase I Closed Conformation 2 (CC2)== |
| <StructureSection load='6rql' size='340' side='right'caption='[[6rql]], [[Resolution|resolution]] 2.90Å' scene=''> | | <SX load='6rql' size='340' side='right' viewer='molstar' caption='[[6rql]], [[Resolution|resolution]] 2.90Å' scene=''> |
| == Structural highlights == | | == Structural highlights == |
| <table><tr><td colspan='2'>[[6rql]] is a 20 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6RQL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6RQL FirstGlance]. <br> | | <table><tr><td colspan='2'>[[6rql]] 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=6RQL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6RQL FirstGlance]. <br> |
| </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> | | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 2.9Å</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=6rql FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rql OCA], [http://pdbe.org/6rql PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6rql RCSB], [http://www.ebi.ac.uk/pdbsum/6rql PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6rql ProSAT]</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=6rql FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6rql OCA], [https://pdbe.org/6rql PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6rql RCSB], [https://www.ebi.ac.uk/pdbsum/6rql PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6rql ProSAT]</span></td></tr> |
| </table> | | </table> |
| == Function == | | == Function == |
| [[http://www.uniprot.org/uniprot/RPAB1_YEAST RPAB1_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 small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, RPB5 is part of the lower jaw surrounding the central large cleft and thought to grab the incoming DNA template. Seems to be the major component in this process (By similarity). [[http://www.uniprot.org/uniprot/RPA1_YEAST RPA1_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Largest and catalytic core component of RNA polymerase I which synthesizes ribosomal RNA precursors. Forms the polymerase active center together with the second largest subunit. A single stranded DNA template strand of the promoter is positioned within the central active site cleft of Pol I. A bridging helix emanates from RPA1 and crosses the cleft near the catalytic site and is thought to promote translocation of Pol I by acting as a ratchet that moves the RNA-DNA hybrid through the active site by switching from straight to bent conformations at each step of nucleotide addition (By similarity). [[http://www.uniprot.org/uniprot/RPAC2_YEAST RPAC2_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common core component of RNA polymerases I and III which synthesize ribosomal RNA precursors and small RNAs, such as 5S rRNA and tRNAs, respectively. [[http://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. [[http://www.uniprot.org/uniprot/RPAB5_YEAST RPAB5_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. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, RBP10 is part of the core element with the central large cleft. [[http://www.uniprot.org/uniprot/RPA43_YEAST RPA43_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase I which synthesizes ribosomal RNA precursors. Through its association with RRN3 is involved in recruitment of Pol I to rDNA promoters. In vitro, the A13-A43 subcomplex binds single-stranded RNA.<ref>PMID:11032814</ref> <ref>PMID:12888498</ref> [[http://www.uniprot.org/uniprot/RPA49_YEAST RPA49_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase I which synthesizes ribosomal RNA precursors. A49 is easily dissociated from the rest of pol A (pol I), producing the form A*, which shows impaired transcriptional activity and increased sensitivity to alpha-amanitin. The function of A49 might be linked to the RNase H activity that was found associated with this subunit. [[http://www.uniprot.org/uniprot/RRN7_YEAST RRN7_YEAST]] Component of RNA polymerase I core factor complex (CF) that acts as a SUA7/TFIIB-like factor and plays a key role in multiple steps during transcription initiation such as pre-initiation complex (PIC) assembly and postpolymerase recruitment events in polymerase I (Pol I) transcription. Binds rDNA promoters and plays a role in Pol I recruitment. After binding of UAF (upstream activation factor) to an upstream element of the promoter, CF is recruited in a SPT15/TBP-dependent manner to form a pre-initiation complex.<ref>PMID:21921198</ref> <ref>PMID:21940764</ref> <ref>PMID:8887672</ref> [[http://www.uniprot.org/uniprot/RPAC1_YEAST RPAC1_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 and III which synthesize ribosomal RNA precursors and small RNAs, such as 5S rRNA and tRNAs, respectively. RPAC1 is part of the Pol core element with the central large cleft and probably a clamp element that moves to open and close the cleft (By similarity). [[http://www.uniprot.org/uniprot/RPAB2_YEAST RPAB2_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 small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, RPB6 is part of the clamp element and togther with parts of RPB1 and RPB2 forms a pocket to which the RPB4-RPB7 subcomplex binds (By similarity). [[http://www.uniprot.org/uniprot/RRN3_YEAST RRN3_YEAST]] Required for efficient transcription initiation by RNA polymerase I. Interacts with Pol I in the absence of template DNA and stimulates recruitment of Pol I, but does not remain as part of stable preinitiation complex. [[http://www.uniprot.org/uniprot/RPAB3_YEAST RPAB3_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 small RNAs, such as 5S rRNA and tRNAs, respectively. [[http://www.uniprot.org/uniprot/RPA12_YEAST RPA12_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase I which synthesizes ribosomal RNA precursors. Involved in transcriptional termination. Involved in recruitment of RPA49 to Pol I.<ref>PMID:15073335</ref> [[http://www.uniprot.org/uniprot/RPA2_YEAST RPA2_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Second largest core component of RNA polymerase I which synthesizes ribosomal RNA precursors. Proposed to contribute to the polymerase catalytic activity and forms the polymerase active center together with the largest subunit. Pol I is composed of mobile elements and RPA2 is part of the core element with the central large cleft and probably a clamp element that moves to open and close the cleft (By similarity). [[http://www.uniprot.org/uniprot/RRN6_YEAST RRN6_YEAST]] Acts as component of the core factor (CF) complex which is essential for the initiation of rDNA transcription by RNA polymerase I. After binding of UAF (upstream activation factor) to an upstream element of the promoter, CF is recruited in a SPT15/TBP-dependent manner to form a preinitiation complex.<ref>PMID:8887672</ref> [[http://www.uniprot.org/uniprot/RPA34_YEAST RPA34_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase I which synthesizes ribosomal RNA precursors.<ref>PMID:9121426</ref> [[http://www.uniprot.org/uniprot/RPA14_YEAST RPA14_YEAST]] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase I which synthesizes ribosomal RNA precursors. A14 seems to play a role in the stability of subunits ABC23 and A43. In vitro, the A14-A43 subcomplex binds single-stranded RNA.<ref>PMID:12888498</ref> [[http://www.uniprot.org/uniprot/RRN11_YEAST RRN11_YEAST]] Acts as component of the core factor (CF) complex which is essential for the initiation of rDNA transcription by RNA polymerase I. After binding of UAF (upstream activation factor) to an upstream element of the promoter, CF is recruited in a SPT15/TBP-dependent manner to form a preinitiation complex.<ref>PMID:8887672</ref> | | [https://www.uniprot.org/uniprot/RRN7_YEAST RRN7_YEAST] Component of RNA polymerase I core factor complex (CF) that acts as a SUA7/TFIIB-like factor and plays a key role in multiple steps during transcription initiation such as pre-initiation complex (PIC) assembly and postpolymerase recruitment events in polymerase I (Pol I) transcription. Binds rDNA promoters and plays a role in Pol I recruitment. After binding of UAF (upstream activation factor) to an upstream element of the promoter, CF is recruited in a SPT15/TBP-dependent manner to form a pre-initiation complex.<ref>PMID:21921198</ref> <ref>PMID:21940764</ref> <ref>PMID:8887672</ref> |
| | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == |
| | RNA polymerase I (Pol I) assembles with core factor (CF) and Rrn3 on the rDNA core promoter for transcription initiation. Here, we report cryo-EM structures of closed, intermediate and open Pol I initiation complexes from 2.7 to 3.7 A resolution to visualize Pol I promoter melting and to structurally and biochemically characterize the recognition mechanism of Pol I promoter DNA. In the closed complex, double-stranded DNA runs outside the DNA-binding cleft. Rotation of CF and upstream DNA with respect to Pol I and Rrn3 results in the spontaneous loading and opening of the promoter followed by cleft closure and positioning of the Pol I A49 tandem winged helix domain (tWH) onto DNA. Conformational rearrangement of A49 tWH leads to a clash with Rrn3 to initiate complex disassembly and promoter escape. Comprehensive insight into the Pol I transcription initiation cycle allows comparisons with promoter opening by Pol II and Pol III. |
| | |
| | Molecular insight into RNA polymerase I promoter recognition and promoter melting.,Sadian Y, Baudin F, Tafur L, Murciano B, Wetzel R, Weis F, Muller CW Nat Commun. 2019 Dec 5;10(1):5543. doi: 10.1038/s41467-019-13510-w. PMID:31804486<ref>PMID:31804486</ref> |
| | |
| | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> |
| | <div class="pdbe-citations 6rql" style="background-color:#fffaf0;"></div> |
| | |
| | ==See Also== |
| | *[[RNA polymerase 3D structures|RNA polymerase 3D structures]] |
| | *[[Transcription initiation factors 3D structures|Transcription initiation factors 3D structures]] |
| == References == | | == References == |
| <references/> | | <references/> |
| __TOC__ | | __TOC__ |
| </StructureSection> | | </SX> |
| [[Category: DNA-directed RNA polymerase]]
| |
| [[Category: Large Structures]] | | [[Category: Large Structures]] |
| [[Category: Mueller, C W]] | | [[Category: Saccharomyces cerevisiae]] |
| [[Category: Sadian, Y]] | | [[Category: Synthetic construct]] |
| [[Category: Tafur, L]] | | [[Category: Mueller CW]] |
| [[Category: Cc]] | | [[Category: Sadian Y]] |
| [[Category: Cf]] | | [[Category: Tafur L]] |
| [[Category: Closed complex]]
| |
| [[Category: Core factor]]
| |
| [[Category: Pic]]
| |
| [[Category: Pre-initiation complex]]
| |
| [[Category: Rna polymerase i]]
| |
| [[Category: Rrn3]]
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| [[Category: Transcription]]
| |