8xmc: Difference between revisions

Latest revision as of 06:36, 24 July 2024

Post-translocated Pol IV transcription elongation complex

Structural highlights

8xmc 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 3.1Å
Ligands:	MG, ZN
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]

References

↑ 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
↑ 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
↑ 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:https://dx.doi.org/10.1126/science.1106910
↑ 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
↑ 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
↑ 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:https://dx.doi.org/10.1038/ng1675
↑ 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
↑ 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
↑ 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
↑ 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:https://dx.doi.org/10.1105/tpc.107.051540
↑ 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
↑ 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:https://dx.doi.org/10.1073/pnas.0706701104
↑ 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
↑ 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
↑ 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
↑ 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

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OCA

[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:https://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:https://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:https://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:https://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

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 8xmc is ON HOLD  until Paper Publication
+==Post-translocated Pol IV transcription elongation complex==
+<StructureSection load='8xmc' size='340' side='right'caption='[[8xmc]], [[Resolution|resolution]] 3.10&Aring;' scene=''>
-Authors: Huang, K., Fang, C.L., Zhang, Y.
+== Structural highlights ==
+<table><tr><td colspan='2'>[[8xmc]] 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=8XMC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8XMC FirstGlance]. <br>
-Description: Post-translocated Pol IV transcription elongation complex
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.1&#8491;</td></tr>
-[[Category: Unreleased Structures]]
+<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>
-[[Category: Zhang, Y]]
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=8xmc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8xmc OCA], [https://pdbe.org/8xmc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8xmc RCSB], [https://www.ebi.ac.uk/pdbsum/8xmc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8xmc ProSAT]</span></td></tr>
-[[Category: Fang, C.L]]
+</table>
-[[Category: Huang, K]]
+== 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>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Arabidopsis thaliana]]
+[[Category: Large Structures]]
+[[Category: Fang CL]]
+[[Category: Huang K]]
+[[Category: Zhang Y]]

8xmc: Difference between revisions

Latest revision as of 06:36, 24 July 2024

Post-translocated Pol IV transcription elongation complex

Structural highlights

Function

References

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