7eu0: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older edit
No edit summary
No edit summary
 
(2 intermediate revisions by the same user not shown)
Line 1: Line 1:
'''Unreleased structure'''


The entry 7eu0 is ON HOLD
==The cryo-EM structure of A. thaliana Pol IV-RDR2 backtracked complex==
<StructureSection load='7eu0' size='340' side='right'caption='[[7eu0]], [[Resolution|resolution]] 3.16&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[7eu0]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7EU0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7EU0 FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.16&#8491;</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=7eu0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7eu0 OCA], [https://pdbe.org/7eu0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7eu0 RCSB], [https://www.ebi.ac.uk/pdbsum/7eu0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7eu0 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/NRPD1_ARATH NRPD1_ARATH] DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates (By similarity). Largest and catalytic component of RNA polymerase IV which mediates 24-nt short-interfering RNAs (siRNA) accumulation. Implicated in siRNA-directed heterochromatin formation through the action of DCL3 and AGO4, and subsequent DNA methylation-dependent silencing of targeted sequences. Essential component of a self-reinforcing loop coupling de novo DNA methylation to siRNA production. Required for intercellular but not intracellular RNA interference (RNAi) leading to systemic post-transcriptional gene silencing. Involved in the maintenance of post-transcriptional RNA silencing.<ref>PMID:10850496</ref> <ref>PMID:12198169</ref> <ref>PMID:15692015</ref> <ref>PMID:15766525</ref> <ref>PMID:16140984</ref> <ref>PMID:16273107</ref> <ref>PMID:16377568</ref> <ref>PMID:16839878</ref> <ref>PMID:17360559</ref> <ref>PMID:17526749</ref> <ref>PMID:17558406</ref> <ref>PMID:17785412</ref> <ref>PMID:18287047</ref> <ref>PMID:18433438</ref> <ref>PMID:18467467</ref> <ref>PMID:19110459</ref>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
DNA methylation affects gene expression and maintains genome integrity. The DNA-dependent RNA polymerase IV (Pol IV), together with the RNA-dependent RNA polymerase RDR2, produces double-stranded small interfering RNA precursors essential for establishing and maintaining DNA methylation in plants. We determined the cryo-electron microscopy structures of the Pol IV-RDR2 holoenzyme and the backtracked transcription elongation complex. These structures reveal that Pol IV and RDR2 form a complex with their active sites connected by an interpolymerase channel, through which the Pol IV-generated transcript is handed over to the RDR2 active site after being backtracked, where it is used as the template for double-stranded RNA (dsRNA) synthesis. Our results describe a 'backtracking-triggered RNA channeling' mechanism underlying dsRNA synthesis and also shed light on the evolutionary trajectory of eukaryotic RNA polymerases.


Authors: Fang, C.L., Wu, X.X., Huang, K., Zhang, Y.
Pol IV and RDR2: A two-RNA-polymerase machine that produces double-stranded RNA.,Huang K, Wu XX, Fang CL, Xu ZG, Zhang HW, Gao J, Zhou CM, You LL, Gu ZX, Mu WH, Feng Y, Wang JW, Zhang Y Science. 2021 Dec 24;374(6575):1579-1586. doi: 10.1126/science.abj9184. Epub 2021 , Dec 23. PMID:34941388<ref>PMID:34941388</ref>


Description: The cryo-EM structure of A. thaliana Pol IV-RDR2 backtracked complex
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
[[Category: Unreleased Structures]]
</div>
[[Category: Zhang, Y]]
<div class="pdbe-citations 7eu0" style="background-color:#fffaf0;"></div>
[[Category: Wu, X.X]]
 
[[Category: Huang, K]]
==See Also==
[[Category: Fang, C.L]]
*[[RNA polymerase 3D structures|RNA polymerase 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Arabidopsis thaliana]]
[[Category: Large Structures]]
[[Category: Fang CL]]
[[Category: Huang K]]
[[Category: Wu XX]]
[[Category: Zhang Y]]

Latest revision as of 08:44, 5 June 2024

The cryo-EM structure of A. thaliana Pol IV-RDR2 backtracked complexThe cryo-EM structure of A. thaliana Pol IV-RDR2 backtracked complex

Structural highlights

7eu0 is a 10 chain structure with sequence from Arabidopsis thaliana. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:Electron Microscopy, Resolution 3.16Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

NRPD1_ARATH DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates (By similarity). Largest and catalytic component of RNA polymerase IV which mediates 24-nt short-interfering RNAs (siRNA) accumulation. Implicated in siRNA-directed heterochromatin formation through the action of DCL3 and AGO4, and subsequent DNA methylation-dependent silencing of targeted sequences. Essential component of a self-reinforcing loop coupling de novo DNA methylation to siRNA production. Required for intercellular but not intracellular RNA interference (RNAi) leading to systemic post-transcriptional gene silencing. Involved in the maintenance of post-transcriptional RNA silencing.[1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16]

Publication Abstract from PubMed

DNA methylation affects gene expression and maintains genome integrity. The DNA-dependent RNA polymerase IV (Pol IV), together with the RNA-dependent RNA polymerase RDR2, produces double-stranded small interfering RNA precursors essential for establishing and maintaining DNA methylation in plants. We determined the cryo-electron microscopy structures of the Pol IV-RDR2 holoenzyme and the backtracked transcription elongation complex. These structures reveal that Pol IV and RDR2 form a complex with their active sites connected by an interpolymerase channel, through which the Pol IV-generated transcript is handed over to the RDR2 active site after being backtracked, where it is used as the template for double-stranded RNA (dsRNA) synthesis. Our results describe a 'backtracking-triggered RNA channeling' mechanism underlying dsRNA synthesis and also shed light on the evolutionary trajectory of eukaryotic RNA polymerases.

Pol IV and RDR2: A two-RNA-polymerase machine that produces double-stranded RNA.,Huang K, Wu XX, Fang CL, Xu ZG, Zhang HW, Gao J, Zhou CM, You LL, Gu ZX, Mu WH, Feng Y, Wang JW, Zhang Y Science. 2021 Dec 24;374(6575):1579-1586. doi: 10.1126/science.abj9184. Epub 2021 , Dec 23. PMID:34941388[17]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

See Also

References

  1. ↑ Dalmay T, Hamilton A, Rudd S, Angell S, Baulcombe DC. An RNA-dependent RNA polymerase gene in Arabidopsis is required for posttranscriptional gene silencing mediated by a transgene but not by a virus. Cell. 2000 May 26;101(5):543-53. PMID:10850496 doi:10.1016/s0092-8674(00)80864-8
  2. ↑ Hamilton A, Voinnet O, Chappell L, Baulcombe D. Two classes of short interfering RNA in RNA silencing. EMBO J. 2002 Sep 2;21(17):4671-9. PMID:12198169 doi:10.1093/emboj/cdf464
  3. ↑ Herr AJ, Jensen MB, Dalmay T, Baulcombe DC. RNA polymerase IV directs silencing of endogenous DNA. Science. 2005 Apr 1;308(5718):118-20. doi: 10.1126/science.1106910. Epub 2005 Feb, 3. PMID:15692015 doi:http://dx.doi.org/10.1126/science.1106910
  4. ↑ Onodera Y, Haag JR, Ream T, Costa Nunes P, Pontes O, Pikaard CS. Plant nuclear RNA polymerase IV mediates siRNA and DNA methylation-dependent heterochromatin formation. Cell. 2005 Mar 11;120(5):613-22. PMID:15766525 doi:10.1016/j.cell.2005.02.007
  5. ↑ Pontier D, Yahubyan G, Vega D, Bulski A, Saez-Vasquez J, Hakimi MA, Lerbs-Mache S, Colot V, Lagrange T. Reinforcement of silencing at transposons and highly repeated sequences requires the concerted action of two distinct RNA polymerases IV in Arabidopsis. Genes Dev. 2005 Sep 1;19(17):2030-40. PMID:16140984 doi:10.1101/gad.348405
  6. ↑ Dunoyer P, Himber C, Voinnet O. DICER-LIKE 4 is required for RNA interference and produces the 21-nucleotide small interfering RNA component of the plant cell-to-cell silencing signal. Nat Genet. 2005 Dec;37(12):1356-60. Epub 2005 Nov 6. PMID:16273107 doi:http://dx.doi.org/10.1038/ng1675
  7. ↑ Borsani O, Zhu J, Verslues PE, Sunkar R, Zhu JK. Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis. Cell. 2005 Dec 29;123(7):1279-91. PMID:16377568 doi:10.1016/j.cell.2005.11.035
  8. ↑ Pontes O, Li CF, Costa Nunes P, Haag J, Ream T, Vitins A, Jacobsen SE, Pikaard CS. The Arabidopsis chromatin-modifying nuclear siRNA pathway involves a nucleolar RNA processing center. Cell. 2006 Jul 14;126(1):79-92. PMID:16839878 doi:10.1016/j.cell.2006.05.031
  9. ↑ Zhang X, Henderson IR, Lu C, Green PJ, Jacobsen SE. Role of RNA polymerase IV in plant small RNA metabolism. Proc Natl Acad Sci U S A. 2007 Mar 13;104(11):4536-41. PMID:17360559 doi:10.1073/pnas.0611456104
  10. ↑ Smith LM, Pontes O, Searle I, Yelina N, Yousafzai FK, Herr AJ, Pikaard CS, Baulcombe DC. An SNF2 protein associated with nuclear RNA silencing and the spread of a silencing signal between cells in Arabidopsis. Plant Cell. 2007 May;19(5):1507-21. doi: 10.1105/tpc.107.051540. Epub 2007 May, 25. PMID:17526749 doi:http://dx.doi.org/10.1105/tpc.107.051540
  11. ↑ Dunoyer P, Himber C, Ruiz-Ferrer V, Alioua A, Voinnet O. Intra components of the microRNA and heterochromatic silencing pathways. Nat Genet. 2007 Jul;39(7):848-56. PMID:17558406 doi:10.1038/ng2081
  12. ↑ Brosnan CA, Mitter N, Christie M, Smith NA, Waterhouse PM, Carroll BJ. Nuclear gene silencing directs reception of long-distance mRNA silencing in Arabidopsis. Proc Natl Acad Sci U S A. 2007 Sep 11;104(37):14741-6. doi:, 10.1073/pnas.0706701104. Epub 2007 Sep 4. PMID:17785412 doi:http://dx.doi.org/10.1073/pnas.0706701104
  13. ↑ Mosher RA, Schwach F, Studholme D, Baulcombe DC. PolIVb influences RNA-directed DNA methylation independently of its role in siRNA biogenesis. Proc Natl Acad Sci U S A. 2008 Feb 26;105(8):3145-50. PMID:18287047 doi:10.1073/pnas.0709632105
  14. ↑ Eamens A, Vaistij FE, Jones L. NRPD1a and NRPD1b are required to maintain post-transcriptional RNA silencing and RNA-directed DNA methylation in Arabidopsis. Plant J. 2008 Aug;55(4):596-606. PMID:18433438 doi:10.1111/j.1365-313X.2008.03525.x
  15. ↑ Pérez-Hormaeche J, Potet F, Beauclair L, Le Masson I, Courtial B, Bouché N, Lucas H. Invasion of the Arabidopsis genome by the tobacco retrotransposon Tnt1 is controlled by reversible transcriptional gene silencing. Plant Physiol. 2008 Jul;147(3):1264-78. PMID:18467467 doi:10.1104/pp.108.117846
  16. ↑ Ream TS, Haag JR, Wierzbicki AT, Nicora CD, Norbeck AD, Zhu JK, Hagen G, Guilfoyle TJ, Pasa-Tolić L, Pikaard CS. Subunit compositions of the RNA-silencing enzymes Pol IV and Pol V reveal their origins as specialized forms of RNA polymerase II. Mol Cell. 2009 Jan 30;33(2):192-203. PMID:19110459 doi:10.1016/j.molcel.2008.12.015
  17. ↑ Huang K, Wu XX, Fang CL, Xu ZG, Zhang HW, Gao J, Zhou CM, You LL, Gu ZX, Mu WH, Feng Y, Wang JW, Zhang Y. Pol IV and RDR2: A two-RNA-polymerase machine that produces double-stranded RNA. Science. 2021 Dec 24;374(6575):1579-1586. PMID:34941388 doi:10.1126/science.abj9184

7eu0, resolution 3.16Å

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=7eu0&oldid=4230744"