This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

2n3h

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

Solution structure of DRB4 dsRBD2 (viz. DRB4(81-151))

Structural highlights

2n3h is a 1 chain structure with sequence from Arabidopsis thaliana. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Solution NMR
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

DRB4_ARATH Double-stranded RNA-binding protein involved in RNA-mediated post-transcriptional gene silencing (PTGS). Functions in the trans-acting small interfering RNAs (ta-siRNAs) biogenesis by binding and assisting DICER-LIKE 4 (DCL4). Required for DCL4 activity. Required for the 21 nucleotide ta-siRNAs production of the TAS3 transcript in leaves but not in flowers. Plays an important role in silencing RNA of both DNA and RNA viruses. Involved with argonaute 7 (AGO7) and RDR6 in turnip crinkle virus (TCV) silencing. May not be directly involved in viral siRNA production. May stabilize the 21 nucleotide viral siRNAs and deliver them to the RISC complex. Targeted by the viral silencing suppressor (VSR) transactivator/viroplasmin (TAV) protein of the cauliflower mosaic virus (CaMV) that inactivates DRB4 function in RNA silencing. Probably not involved in the guide strand selection from RNA duplexes. Involved in leaf morphology through its function in ta-siRNA-mediated silencing.^[1] ^[2] ^[3] ^[4]

Publication Abstract from PubMed

In Arabidopsis thaliana, endogenous trans-acting and exogenous siRNA pathways are initiated by the interaction of DRB4 with trigger dsRNA. Further, DCL4:DRB4 complex cleaves the dsRNA into 21 bp siRNA. Understanding molecular determinants and mechanistic details of dsRNA recognition by DRB4 is vital for inducing long-term RNAi-mediated gene regulation in plants. Here, we present solution structures of individual and concatenated DRB4 dsRBDs and demonstrate modes of dsRNA binding by employing NMR, ITC and site-specific mutagenesis. While both dsRBDs adopt the canonical alpha-beta-beta-beta-alpha fold, key structural differences and ms-mus dynamics located at the RNA binding region were observed for dsRBD1. These features favor dsRBD1 to orient itself and make stronger tripartite contact with dsRNA, a feature missing in dsRBD2. Additionally, the inter-domain orientation induced by the linker restricts the mobility of dsRBD2, resulting in the steric hindrance of alpha1 helix in dsRBD2, and leads in further reduction of its dsRNA binding activity. Our study deciphers functional roles of DRB4 domains by showing that dsRBD1 drives the tasiRNA/siRNA pathway. Furthermore, we identify a potential role of the C-terminal region of DRB4 in protein:protein interaction as it possesses six PxxP motifs, binds to Zn2+ and contains a small structural domain.

DRB4 dsRBD1 drives dsRNA recognition in Arabidopsis thaliana tasi/siRNA pathway.,Chiliveri SC, Aute R, Rai U, Deshmukh MV Nucleic Acids Res. 2017 Aug 21;45(14):8551-8563. doi: 10.1093/nar/gkx481. PMID:28575480^[5]

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

References

↑ Adenot X, Elmayan T, Lauressergues D, Boutet S, Bouche N, Gasciolli V, Vaucheret H. DRB4-dependent TAS3 trans-acting siRNAs control leaf morphology through AGO7. Curr Biol. 2006 May 9;16(9):927-32. PMID:16682354 doi:http://dx.doi.org/10.1016/j.cub.2006.03.035
↑ Nakazawa Y, Hiraguri A, Moriyama H, Fukuhara T. The dsRNA-binding protein DRB4 interacts with the Dicer-like protein DCL4 in vivo and functions in the trans-acting siRNA pathway. Plant Mol Biol. 2007 Apr;63(6):777-85. Epub 2007 Jan 14. PMID:17221360 doi:http://dx.doi.org/10.1007/s11103-006-9125-8
↑ Curtin SJ, Watson JM, Smith NA, Eamens AL, Blanchard CL, Waterhouse PM. The roles of plant dsRNA-binding proteins in RNAi-like pathways. FEBS Lett. 2008 Aug 6;582(18):2753-60. doi: 10.1016/j.febslet.2008.07.004. Epub, 2008 Jul 14. PMID:18625233 doi:http://dx.doi.org/10.1016/j.febslet.2008.07.004
↑ Qu F, Ye X, Morris TJ. Arabidopsis DRB4, AGO1, AGO7, and RDR6 participate in a DCL4-initiated antiviral RNA silencing pathway negatively regulated by DCL1. Proc Natl Acad Sci U S A. 2008 Sep 23;105(38):14732-7. doi:, 10.1073/pnas.0805760105. Epub 2008 Sep 17. PMID:18799732 doi:http://dx.doi.org/10.1073/pnas.0805760105
↑ Chiliveri SC, Aute R, Rai U, Deshmukh MV. DRB4 dsRBD1 drives dsRNA recognition in Arabidopsis thaliana tasi/siRNA pathway. Nucleic Acids Res. 2017 Aug 21;45(14):8551-8563. doi: 10.1093/nar/gkx481. PMID:28575480 doi:http://dx.doi.org/10.1093/nar/gkx481

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2n3h"

Categories: Arabidopsis thaliana | Large Structures | Chiliveri S | Deshmukh M

@@ Line 4: / Line 4: @@
 == Structural highlights ==
 <table><tr><td colspan='2'>[[2n3h]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2N3H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2N3H FirstGlance]. <br>
-</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=2n3h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2n3h OCA], [https://pdbe.org/2n3h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2n3h RCSB], [https://www.ebi.ac.uk/pdbsum/2n3h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2n3h ProSAT]</span></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</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=2n3h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2n3h OCA], [https://pdbe.org/2n3h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2n3h RCSB], [https://www.ebi.ac.uk/pdbsum/2n3h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2n3h ProSAT]</span></td></tr>
 </table>
 == Function ==

2n3h

From Proteopedia

Current revision

Solution structure of DRB4 dsRBD2 (viz. DRB4(81-151))

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox