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.

2q3t

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At3g22680

Structural highlights

2q3t 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 1.6Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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

X-ray crystallography typically uses a single set of coordinates and B factors to describe macromolecular conformations. Refinement of multiple copies of the entire structure has been previously used in specific cases as an alternative means of representing structural flexibility. Here, we systematically validate this method by using simulated diffraction data, and we find that ensemble refinement produces better representations of the distributions of atomic positions in the simulated structures than single-conformer refinements. Comparison of principal components calculated from the refined ensembles and simulations shows that concerted motions are captured locally, but that correlations dissipate over long distances. Ensemble refinement is also used on 50 experimental structures of varying resolution and leads to decreases in R(free) values, implying that improvements in the representation of flexibility observed for the simulated structures may apply to real structures. These gains are essentially independent of resolution or data-to-parameter ratio, suggesting that even structures at moderate resolution can benefit from ensemble refinement.

Ensemble refinement of protein crystal structures: validation and application.,Levin EJ, Kondrashov DA, Wesenberg GE, Phillips GN Jr Structure. 2007 Sep;15(9):1040-52. PMID:17850744^[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:http://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:http://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:http://dx.doi.org/10.1038/nsmb.2354
↑ Levin EJ, Kondrashov DA, Wesenberg GE, Phillips GN Jr. Ensemble refinement of protein crystal structures: validation and application. Structure. 2007 Sep;15(9):1040-52. PMID:17850744 doi:http://dx.doi.org/10.1016/j.str.2007.06.019

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/2q3t"

@@ Line 1: / Line 1: @@
 ==Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At3g22680==
-<StructureSection load='2q3t' size='340' side='right' caption='[[2q3t]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
+<StructureSection load='2q3t' size='340' side='right'caption='[[2q3t]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2q3t]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q3T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2Q3T FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2q3t]] 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=2Q3T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q3T FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.6&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1vk5|1vk5]]</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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">At3g22680, MWI23.5 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 Arabidopsis thaliana])</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=2q3t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q3t OCA], [https://pdbe.org/2q3t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q3t RCSB], [https://www.ebi.ac.uk/pdbsum/2q3t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q3t ProSAT]</span></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=2q3t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q3t OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2q3t RCSB], [http://www.ebi.ac.uk/pdbsum/2q3t PDBsum]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/Y3268_ARATH Y3268_ARATH]] Regulator of RNA-directed DNA methylation (RdDM). Binds to single-stranded methyl DNA.
+[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 ==
@@ Line 18: / Line 18: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2q3t" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
@@ Line 23: / Line 24: @@
 </StructureSection>
 [[Category: Arabidopsis thaliana]]
-[[Category: Structural genomic]]
+[[Category: Large Structures]]
-[[Category: Kondrashov, D A]]
+[[Category: Kondrashov DA]]
-[[Category: Levin, E J]]
+[[Category: Levin EJ]]
-[[Category: Phillips, G N]]
+[[Category: Phillips Jr GN]]
-[[Category: Wesenberg, G E]]
+[[Category: Wesenberg GE]]
-[[Category: Cesg]]
-[[Category: Ensemble refinement]]
-[[Category: PSI, Protein structure initiative]]
-[[Category: Refinement methodology development]]
-[[Category: Unknown function]]

2q3t

From Proteopedia

Current revision

Ensemble refinement of the protein crystal structure of gene product from Arabidopsis thaliana At3g22680

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox