5zuu: Difference between revisions

Revision as of 07:19, 21 May 2019

Crystal structure of AtCPSF30 YTH domain in complex with 10mer m6A-modified RNA

Structural highlights

5zuu is a 8 chain structure with sequence from Arath. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	EPE, GOL
NonStd Res:	6MD
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[CPSF_ARATH] Component of the cleavage and polyadenylation specificity factor (CPSF) complex that play a key role in pre-mRNA 3'-end formation. May interact with poly(A) polymerase and other factors to bring about cleavage and poly(A) addition (By similarity). Mediates poly(A) site selection (PubMed:23136375). Binds RNA in a calcium-dependent manner (PubMed:16500995, PubMed:17576667, PubMed:20214900). Exhibits endonuclease activity with an ability to nick and degrade linear as well as circular single-stranded RNA that leaves RNA 3' ends with hydroxyl groups, thus mediating processing of the pre-mRNA as a prelude to the polyadenylation (PubMed:17576667). Involved in the post-transcriptional control, probably via poly(A) addition, of the responses of plants to stress, especially genes mediating tolerance to oxidative stress (PubMed:18545667). Plays a role in the regulation of salicylic acid (SA) production via the control of messenger RNA 3' end processing, thus being a key component of programmed cell death and plant immune responses required for resistance to virulent Pseudomonas syringae pv tomato DC3000 (Pst) (PubMed:24706550).[UniProtKB:O95639]^[1] ^[2] ^[3] ^[4] ^[5] ^[6]

References

↑ Delaney KJ, Xu R, Zhang J, Li QQ, Yun KY, Falcone DL, Hunt AG. Calmodulin interacts with and regulates the RNA-binding activity of an Arabidopsis polyadenylation factor subunit. Plant Physiol. 2006 Apr;140(4):1507-21. doi: 10.1104/pp.105.070672. Epub 2006 Feb, 24. PMID:16500995 doi:https://dx.doi.org/10.1104/pp.105.070672
↑ Addepalli B, Hunt AG. A novel endonuclease activity associated with the Arabidopsis ortholog of the 30-kDa subunit of cleavage and polyadenylation specificity factor. Nucleic Acids Res. 2007;35(13):4453-63. doi: 10.1093/nar/gkm457. Epub 2007 Jun, 18. PMID:17576667 doi:https://dx.doi.org/10.1093/nar/gkm457
↑ Zhang J, Addepalli B, Yun KY, Hunt AG, Xu R, Rao S, Li QQ, Falcone DL. A polyadenylation factor subunit implicated in regulating oxidative signaling in Arabidopsis thaliana. PLoS One. 2008 Jun 11;3(6):e2410. doi: 10.1371/journal.pone.0002410. PMID:18545667 doi:https://dx.doi.org/10.1371/journal.pone.0002410
↑ Bell SA, Hunt AG. The Arabidopsis ortholog of the 77 kDa subunit of the cleavage stimulatory factor (AtCstF-77) involved in mRNA polyadenylation is an RNA-binding protein. FEBS Lett. 2010 Apr 16;584(8):1449-54. doi: 10.1016/j.febslet.2010.03.007. Epub, 2010 Mar 6. PMID:20214900 doi:https://dx.doi.org/10.1016/j.febslet.2010.03.007
↑ Thomas PE, Wu X, Liu M, Gaffney B, Ji G, Li QQ, Hunt AG. Genome-wide control of polyadenylation site choice by CPSF30 in Arabidopsis. Plant Cell. 2012 Nov;24(11):4376-88. doi: 10.1105/tpc.112.096107. Epub 2012 Nov, 6. PMID:23136375 doi:https://dx.doi.org/10.1105/tpc.112.096107
↑ Bruggeman Q, Garmier M, de Bont L, Soubigou-Taconnat L, Mazubert C, Benhamed M, Raynaud C, Bergounioux C, Delarue M. The Polyadenylation Factor Subunit CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR30: A Key Factor of Programmed Cell Death and a Regulator of Immunity in Arabidopsis. Plant Physiol. 2014 Jun;165(2):732-746. doi: 10.1104/pp.114.236083. Epub 2014 Apr, 4. PMID:24706550 doi:https://dx.doi.org/10.1104/pp.114.236083

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OCA

[1] Delaney KJ, Xu R, Zhang J, Li QQ, Yun KY, Falcone DL, Hunt AG. Calmodulin interacts with and regulates the RNA-binding activity of an Arabidopsis polyadenylation factor subunit. Plant Physiol. 2006 Apr;140(4):1507-21. doi: 10.1104/pp.105.070672. Epub 2006 Feb, 24. PMID:16500995 doi:https://dx.doi.org/10.1104/pp.105.070672

[2] Addepalli B, Hunt AG. A novel endonuclease activity associated with the Arabidopsis ortholog of the 30-kDa subunit of cleavage and polyadenylation specificity factor. Nucleic Acids Res. 2007;35(13):4453-63. doi: 10.1093/nar/gkm457. Epub 2007 Jun, 18. PMID:17576667 doi:https://dx.doi.org/10.1093/nar/gkm457

[3] Zhang J, Addepalli B, Yun KY, Hunt AG, Xu R, Rao S, Li QQ, Falcone DL. A polyadenylation factor subunit implicated in regulating oxidative signaling in Arabidopsis thaliana. PLoS One. 2008 Jun 11;3(6):e2410. doi: 10.1371/journal.pone.0002410. PMID:18545667 doi:https://dx.doi.org/10.1371/journal.pone.0002410

[4] Bell SA, Hunt AG. The Arabidopsis ortholog of the 77 kDa subunit of the cleavage stimulatory factor (AtCstF-77) involved in mRNA polyadenylation is an RNA-binding protein. FEBS Lett. 2010 Apr 16;584(8):1449-54. doi: 10.1016/j.febslet.2010.03.007. Epub, 2010 Mar 6. PMID:20214900 doi:https://dx.doi.org/10.1016/j.febslet.2010.03.007

[5] Thomas PE, Wu X, Liu M, Gaffney B, Ji G, Li QQ, Hunt AG. Genome-wide control of polyadenylation site choice by CPSF30 in Arabidopsis. Plant Cell. 2012 Nov;24(11):4376-88. doi: 10.1105/tpc.112.096107. Epub 2012 Nov, 6. PMID:23136375 doi:https://dx.doi.org/10.1105/tpc.112.096107

[6] Bruggeman Q, Garmier M, de Bont L, Soubigou-Taconnat L, Mazubert C, Benhamed M, Raynaud C, Bergounioux C, Delarue M. The Polyadenylation Factor Subunit CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR30: A Key Factor of Programmed Cell Death and a Regulator of Immunity in Arabidopsis. Plant Physiol. 2014 Jun;165(2):732-746. doi: 10.1104/pp.114.236083. Epub 2014 Apr, 4. PMID:24706550 doi:https://dx.doi.org/10.1104/pp.114.236083

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 5zuu is ON HOLD  until Paper Publication
+==Crystal structure of AtCPSF30 YTH domain in complex with 10mer m6A-modified RNA==
+<StructureSection load='5zuu' size='340' side='right'caption='[[5zuu]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
-Authors:
+== Structural highlights ==
+<table><tr><td colspan='2'>[[5zuu]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZUU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZUU FirstGlance]. <br>
-Description:
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-[[Category: Unreleased Structures]]
+<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=6MD:N-METHYLADENOSINE'>6MD</scene></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=5zuu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zuu OCA], [http://pdbe.org/5zuu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zuu RCSB], [http://www.ebi.ac.uk/pdbsum/5zuu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zuu ProSAT]</span></td></tr>
+</table>
+== Function ==
+[[http://www.uniprot.org/uniprot/CPSF_ARATH CPSF_ARATH]] Component of the cleavage and polyadenylation specificity factor (CPSF) complex that play a key role in pre-mRNA 3'-end formation. May interact with poly(A) polymerase and other factors to bring about cleavage and poly(A) addition (By similarity). Mediates poly(A) site selection (PubMed:23136375). Binds RNA in a calcium-dependent manner (PubMed:16500995, PubMed:17576667, PubMed:20214900). Exhibits endonuclease activity with an ability to nick and degrade linear as well as circular single-stranded RNA that leaves RNA 3' ends with hydroxyl groups, thus mediating processing of the pre-mRNA as a prelude to the polyadenylation (PubMed:17576667). Involved in the post-transcriptional control, probably via poly(A) addition, of the responses of plants to stress, especially genes mediating tolerance to oxidative stress (PubMed:18545667). Plays a role in the regulation of salicylic acid (SA) production via the control of messenger RNA 3' end processing, thus being a key component of programmed cell death and plant immune responses required for resistance to virulent Pseudomonas syringae pv tomato DC3000 (Pst) (PubMed:24706550).[UniProtKB:O95639]<ref>PMID:16500995</ref> <ref>PMID:17576667</ref> <ref>PMID:18545667</ref> <ref>PMID:20214900</ref> <ref>PMID:23136375</ref> <ref>PMID:24706550</ref>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Arath]]
+[[Category: Large Structures]]
+[[Category: Li, S S]]
+[[Category: Nie, H B]]
+[[Category: Patel, D J]]
+[[Category: Wu, B X]]
+[[Category: Arabidopsis]]
+[[Category: Cpsf]]
+[[Category: Modification]]
+[[Category: Mrna processing]]
+[[Category: Rna binding protein-rna complex]]

5zuu: Difference between revisions

Revision as of 07:19, 21 May 2019

Crystal structure of AtCPSF30 YTH domain in complex with 10mer m6A-modified RNA

Structural highlights

Function

References

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