1vk5: Difference between revisions

Latest revision as of 00:04, 28 December 2023

X-ray Structure of Gene Product from Arabidopsis Thaliana At3g22680

Structural highlights

1vk5 is a 1 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:	X-ray diffraction, Resolution 1.604Å
Ligands:	CPS, EDO, SO4
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT, TOPSAN

Function

RDM1_ARATH Regulator of RNA-directed DNA methylation (RdDM). Binds to single-stranded methyl DNA. Involved in the assembly of RNA polymerase V (Pol V) transcription initiation or elongation complexes at the chromatin, as a componant of the DDR complex.^[1] ^[2] ^[3]

Publication Abstract from PubMed

The gene product of At3g22680 from Arabidopsis thaliana codes for a protein of unknown function. The crystal structure of the At3g22680 gene product was determined by multiple-wavelength anomalous diffraction and refined to an R factor of 16.0% (Rfree = 18.4%) at 1.60 A resolution. The refined structure shows one monomer in the asymmetric unit, with one molecule of the non-denaturing detergent CHAPS {3-[(3-cholamidopropyl)dimethylammonio]-1-propane sulfonate} tightly bound. Protein At3g22680 shows no structural homology to any other known proteins and represents a new fold in protein conformation space.

Structure at 1.6 A resolution of the protein from gene locus At3g22680 from Arabidopsis thaliana.,Allard ST, Bingman CA, Johnson KA, Wesenberg GE, Bitto E, Jeon WB, Phillips GN Jr Acta Crystallogr Sect F Struct Biol Cryst Commun. 2005 Jul 1;61(Pt, 7):647-50. Epub 2005 Jun 30. PMID:16511118^[4]

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

References

↑ Law JA, Ausin I, Johnson LM, Vashisht AA, Zhu JK, Wohlschlegel JA, Jacobsen SE. A protein complex required for polymerase V transcripts and RNA- directed DNA methylation in Arabidopsis. Curr Biol. 2010 May 25;20(10):951-6. doi: 10.1016/j.cub.2010.03.062. Epub 2010, Apr 22. PMID:20409711 doi:https://dx.doi.org/10.1016/j.cub.2010.03.062
↑ Gao Z, Liu HL, Daxinger L, Pontes O, He X, Qian W, Lin H, Xie M, Lorkovic ZJ, Zhang S, Miki D, Zhan X, Pontier D, Lagrange T, Jin H, Matzke AJ, Matzke M, Pikaard CS, Zhu JK. An RNA polymerase II- and AGO4-associated protein acts in RNA-directed DNA methylation. Nature. 2010 May 6;465(7294):106-9. doi: 10.1038/nature09025. Epub 2010 Apr 21. PMID:20410883 doi:https://dx.doi.org/10.1038/nature09025
↑ Zhong X, Hale CJ, Law JA, Johnson LM, Feng S, Tu A, Jacobsen SE. DDR complex facilitates global association of RNA polymerase V to promoters and evolutionarily young transposons. Nat Struct Mol Biol. 2012 Sep;19(9):870-5. doi: 10.1038/nsmb.2354. Epub 2012 Aug , 5. PMID:22864289 doi:https://dx.doi.org/10.1038/nsmb.2354
↑ Allard ST, Bingman CA, Johnson KA, Wesenberg GE, Bitto E, Jeon WB, Phillips GN Jr. Structure at 1.6 A resolution of the protein from gene locus At3g22680 from Arabidopsis thaliana. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2005 Jul 1;61(Pt, 7):647-50. Epub 2005 Jun 30. PMID:16511118 doi:S1744309105019743

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Law JA, Ausin I, Johnson LM, Vashisht AA, Zhu JK, Wohlschlegel JA, Jacobsen SE. A protein complex required for polymerase V transcripts and RNA- directed DNA methylation in Arabidopsis. Curr Biol. 2010 May 25;20(10):951-6. doi: 10.1016/j.cub.2010.03.062. Epub 2010, Apr 22. PMID:20409711 doi:https://dx.doi.org/10.1016/j.cub.2010.03.062

[2] Gao Z, Liu HL, Daxinger L, Pontes O, He X, Qian W, Lin H, Xie M, Lorkovic ZJ, Zhang S, Miki D, Zhan X, Pontier D, Lagrange T, Jin H, Matzke AJ, Matzke M, Pikaard CS, Zhu JK. An RNA polymerase II- and AGO4-associated protein acts in RNA-directed DNA methylation. Nature. 2010 May 6;465(7294):106-9. doi: 10.1038/nature09025. Epub 2010 Apr 21. PMID:20410883 doi:https://dx.doi.org/10.1038/nature09025

[3] Zhong X, Hale CJ, Law JA, Johnson LM, Feng S, Tu A, Jacobsen SE. DDR complex facilitates global association of RNA polymerase V to promoters and evolutionarily young transposons. Nat Struct Mol Biol. 2012 Sep;19(9):870-5. doi: 10.1038/nsmb.2354. Epub 2012 Aug , 5. PMID:22864289 doi:https://dx.doi.org/10.1038/nsmb.2354

[4] Allard ST, Bingman CA, Johnson KA, Wesenberg GE, Bitto E, Jeon WB, Phillips GN Jr. Structure at 1.6 A resolution of the protein from gene locus At3g22680 from Arabidopsis thaliana. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2005 Jul 1;61(Pt, 7):647-50. Epub 2005 Jun 30. PMID:16511118 doi:S1744309105019743

[1]

[2]

[3]

[4]

@@ Line 1: / Line 1: @@
-[[Image:1vk5.gif|left|200px]]<br /><applet load="1vk5" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1vk5, resolution 1.604&Aring;" />
-'''X-ray Structure of Gene Product from Arabidopsis Thaliana At3g22680'''<br />
-==Overview==
+==X-ray Structure of Gene Product from Arabidopsis Thaliana At3g22680==
-The gene product of At3g22680 from Arabidopsis thaliana codes for a, protein of unknown function. The crystal structure of the At3g22680 gene, product was determined by multiple-wavelength anomalous diffraction and, refined to an R factor of 16.0% (Rfree = 18.4%) at 1.60 A resolution. The, refined structure shows one monomer in the asymmetric unit, with one, molecule of the non-denaturing detergent CHAPS, {3-[(3-cholamidopropyl)dimethylammonio]-1-propane sulfonate} tightly, bound. Protein At3g22680 shows no structural homology to any other known, proteins and represents a new fold in protein conformation space.
+<StructureSection load='1vk5' size='340' side='right'caption='[[1vk5]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1vk5]] is a 1 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=1VK5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VK5 FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.604&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CPS:3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE'>CPS</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=1vk5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vk5 OCA], [https://pdbe.org/1vk5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vk5 RCSB], [https://www.ebi.ac.uk/pdbsum/1vk5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vk5 ProSAT], [https://www.topsan.org/Proteins/CESG/1vk5 TOPSAN]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RDM1_ARATH RDM1_ARATH] Regulator of RNA-directed DNA methylation (RdDM). Binds to single-stranded methyl DNA. Involved in the assembly of RNA polymerase V (Pol V) transcription initiation or elongation complexes at the chromatin, as a componant of the DDR complex.<ref>PMID:20409711</ref> <ref>PMID:20410883</ref> <ref>PMID:22864289</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The gene product of At3g22680 from Arabidopsis thaliana codes for a protein of unknown function. The crystal structure of the At3g22680 gene product was determined by multiple-wavelength anomalous diffraction and refined to an R factor of 16.0% (Rfree = 18.4%) at 1.60 A resolution. The refined structure shows one monomer in the asymmetric unit, with one molecule of the non-denaturing detergent CHAPS {3-[(3-cholamidopropyl)dimethylammonio]-1-propane sulfonate} tightly bound. Protein At3g22680 shows no structural homology to any other known proteins and represents a new fold in protein conformation space.
-==About this Structure==
+Structure at 1.6 A resolution of the protein from gene locus At3g22680 from Arabidopsis thaliana.,Allard ST, Bingman CA, Johnson KA, Wesenberg GE, Bitto E, Jeon WB, Phillips GN Jr Acta Crystallogr Sect F Struct Biol Cryst Commun. 2005 Jul 1;61(Pt, 7):647-50. Epub 2005 Jun 30. PMID:16511118<ref>PMID:16511118</ref>
-VK5 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana] with SO4, CPS and EDO as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1VK5 OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Structure at 1.6 A resolution of the protein from gene locus At3g22680 from Arabidopsis thaliana., Allard ST, Bingman CA, Johnson KA, Wesenberg GE, Bitto E, Jeon WB, Phillips GN Jr, Acta Crystallograph Sect F Struct Biol Cryst Commun. 2005 Jul 1;61(Pt, 7):647-50. Epub 2005 Jun 30. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16511118 16511118]
+</div>
+<div class="pdbe-citations 1vk5" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Arabidopsis thaliana]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Allard, S.T.M.]]
+[[Category: Allard STM]]
-[[Category: Bingman, C.A.]]
+[[Category: Bingman CA]]
-[[Category: CESG, Center.for.Eukaryotic.Structural.Genomics.]]
+[[Category: Johnson KA]]
-[[Category: Johnson, K.A.]]
+[[Category: Phillips Jr GN]]
-[[Category: Jr., G.N.Phillips.]]
+[[Category: Smith DW]]
-[[Category: Smith, D.W.]]
+[[Category: Wesenberg GE]]
-[[Category: Wesenberg, G.E.]]
-[[Category: CPS]]
-[[Category: EDO]]
-[[Category: SO4]]
-[[Category: center for eukaryotic structural genomics]]
-[[Category: cesg]]
-[[Category: protein structure initiative]]
-[[Category: psi]]
-[[Category: structural genomics]]
-[[Category: unknown function]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 04:54:56 2007''

1vk5: Difference between revisions

Latest revision as of 00:04, 28 December 2023

X-ray Structure of Gene Product from Arabidopsis Thaliana At3g22680

Structural highlights

Function

Publication Abstract from PubMed

References

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