2rsn: Difference between revisions

Latest revision as of 22:29, 26 March 2025

Solution structure of the chromodomain of Chp1 in complex with H3K9me3 peptide

Structural highlights

2rsn is a 2 chain structure with sequence from Schizosaccharomyces pombe and Schizosaccharomyces pombe 972h-. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Solution NMR, 20 models
Ligands:	M3L
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CHP1_SCHPO Component of the kinetochore which plays a role in stabilizing microtubules and so allowing accurate chromosome segregation. Has a role in the RNA interference (RNAi) pathway which is important for heterochromatin formation and accurate chromosome segregation. A member of the RNA-induced transcriptional silencing (RITS) complex which is involved in the biosynthesis of dsRNA from primer siRNAs provided by the RNA-directed RNA polymerase (RDRC) complex.^[1] ^[2] ^[3] ^[4]

Publication Abstract from PubMed

Centromeric heterochromatin assembly in fission yeast requires the RNAi pathway. Chp1, a chromodomain (CD) protein, forms the Ago1-containing RNA-induced transcriptional silencing (RITS) complex and recruits siRNA-bound RITS to methylated histone H3 lysine 9 (H3K9me) via its CD. Here, we show that the CD of Chp1 (Chp1-CD) possesses unique nucleic acid-binding activities that are essential for heterochromatic gene silencing. Detailed electrophoretic-mobility shift analyses demonstrated that Chp1 binds to RNA via the CD in addition to its central RNA-recognition motif. Interestingly, robust RNA- and DNA-binding activity of Chp1-CD was strongly enhanced when it was bound to H3K9me, which was revealed to involve a positively charged domain within the Chp1-CD by structural analyses. These results demonstrate a role for the CD that provides a link between RNA, DNA, and methylated histone tails to ensure heterochromatic gene silencing.

Intrinsic nucleic Acid-binding activity of chp1 chromodomain is required for heterochromatic gene silencing.,Ishida M, Shimojo H, Hayashi A, Kawaguchi R, Ohtani Y, Uegaki K, Nishimura Y, Nakayama J Mol Cell. 2012 Jul 27;47(2):228-41. Epub 2012 Jun 21. PMID:22727667^[5]

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

References

↑ Doe CL, Wang G, Chow C, Fricker MD, Singh PB, Mellor EJ. The fission yeast chromo domain encoding gene chp1(+) is required for chromosome segregation and shows a genetic interaction with alpha-tubulin. Nucleic Acids Res. 1998 Sep 15;26(18):4222-9. PMID:9722643
↑ Thon G, Verhein-Hansen J. Four chromo-domain proteins of Schizosaccharomyces pombe differentially repress transcription at various chromosomal locations. Genetics. 2000 Jun;155(2):551-68. PMID:10835380
↑ Motamedi MR, Verdel A, Colmenares SU, Gerber SA, Gygi SP, Moazed D. Two RNAi complexes, RITS and RDRC, physically interact and localize to noncoding centromeric RNAs. Cell. 2004 Dec 17;119(6):789-802. PMID:15607976 doi:10.1016/j.cell.2004.11.034
↑ Verdel A, Jia S, Gerber S, Sugiyama T, Gygi S, Grewal SI, Moazed D. RNAi-mediated targeting of heterochromatin by the RITS complex. Science. 2004 Jan 30;303(5658):672-6. Epub 2004 Jan 2. PMID:14704433 doi:10.1126/science.1093686
↑ Ishida M, Shimojo H, Hayashi A, Kawaguchi R, Ohtani Y, Uegaki K, Nishimura Y, Nakayama J. Intrinsic nucleic Acid-binding activity of chp1 chromodomain is required for heterochromatic gene silencing. Mol Cell. 2012 Jul 27;47(2):228-41. Epub 2012 Jun 21. PMID:22727667 doi:10.1016/j.molcel.2012.05.017

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Doe CL, Wang G, Chow C, Fricker MD, Singh PB, Mellor EJ. The fission yeast chromo domain encoding gene chp1(+) is required for chromosome segregation and shows a genetic interaction with alpha-tubulin. Nucleic Acids Res. 1998 Sep 15;26(18):4222-9. PMID:9722643

[2] Thon G, Verhein-Hansen J. Four chromo-domain proteins of Schizosaccharomyces pombe differentially repress transcription at various chromosomal locations. Genetics. 2000 Jun;155(2):551-68. PMID:10835380

[3] Motamedi MR, Verdel A, Colmenares SU, Gerber SA, Gygi SP, Moazed D. Two RNAi complexes, RITS and RDRC, physically interact and localize to noncoding centromeric RNAs. Cell. 2004 Dec 17;119(6):789-802. PMID:15607976 doi:10.1016/j.cell.2004.11.034

[4] Verdel A, Jia S, Gerber S, Sugiyama T, Gygi S, Grewal SI, Moazed D. RNAi-mediated targeting of heterochromatin by the RITS complex. Science. 2004 Jan 30;303(5658):672-6. Epub 2004 Jan 2. PMID:14704433 doi:10.1126/science.1093686

[5] Ishida M, Shimojo H, Hayashi A, Kawaguchi R, Ohtani Y, Uegaki K, Nishimura Y, Nakayama J. Intrinsic nucleic Acid-binding activity of chp1 chromodomain is required for heterochromatic gene silencing. Mol Cell. 2012 Jul 27;47(2):228-41. Epub 2012 Jun 21. PMID:22727667 doi:10.1016/j.molcel.2012.05.017

[1]

[2]

[3]

[4]

[5]

@@ Line 1: / Line 1: @@
 ==Solution structure of the chromodomain of Chp1 in complex with H3K9me3 peptide==
-<StructureSection load='2rsn' size='340' side='right' caption='[[2rsn]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''>
+<StructureSection load='2rsn' size='340' side='right'caption='[[2rsn]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2rsn]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Fission_yeast Fission yeast]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RSN OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2RSN FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2rsn]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Schizosaccharomyces_pombe Schizosaccharomyces pombe] and [https://en.wikipedia.org/wiki/Schizosaccharomyces_pombe_972h- Schizosaccharomyces pombe 972h-]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2RSN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RSN FirstGlance]. <br>
-</td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR, 20 models</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2rso|2rso]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=M3L:N-TRIMETHYLLYSINE'>M3L</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">chp1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=284812 Fission yeast])</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=2rsn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rsn OCA], [https://pdbe.org/2rsn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rsn RCSB], [https://www.ebi.ac.uk/pdbsum/2rsn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rsn 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=2rsn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rsn OCA], [http://pdbe.org/2rsn PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2rsn RCSB], [http://www.ebi.ac.uk/pdbsum/2rsn PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2rsn ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/CHP1_SCHPO CHP1_SCHPO]] Component of the kinetochore which plays a role in stabilizing microtubules and so allowing accurate chromosome segregation. Has a role in the RNA interference (RNAi) pathway which is important for heterochromatin formation and accurate chromosome segregation. A member of the RNA-induced transcriptional silencing (RITS) complex which is involved in the biosynthesis of dsRNA from primer siRNAs provided by the RNA-directed RNA polymerase (RDRC) complex.<ref>PMID:9722643</ref> <ref>PMID:10835380</ref> <ref>PMID:15607976</ref> <ref>PMID:14704433</ref>
+[https://www.uniprot.org/uniprot/CHP1_SCHPO CHP1_SCHPO] Component of the kinetochore which plays a role in stabilizing microtubules and so allowing accurate chromosome segregation. Has a role in the RNA interference (RNAi) pathway which is important for heterochromatin formation and accurate chromosome segregation. A member of the RNA-induced transcriptional silencing (RITS) complex which is involved in the biosynthesis of dsRNA from primer siRNAs provided by the RNA-directed RNA polymerase (RDRC) complex.<ref>PMID:9722643</ref> <ref>PMID:10835380</ref> <ref>PMID:15607976</ref> <ref>PMID:14704433</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 24: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Fission yeast]]
+[[Category: Large Structures]]
-[[Category: Nishimura, Y]]
+[[Category: Schizosaccharomyces pombe]]
-[[Category: Shimojo, H]]
+[[Category: Schizosaccharomyces pombe 972h-]]
-[[Category: Chromodomain]]
+[[Category: Nishimura Y]]
-[[Category: Chromosomal protein]]
+[[Category: Shimojo H]]
-[[Category: Methylation]]
-[[Category: Nuclear protein]]
-[[Category: Protein-peptide complex]]
-[[Category: Rna-mediated gene silencing]]

2rsn: Difference between revisions

Latest revision as of 22:29, 26 March 2025

Solution structure of the chromodomain of Chp1 in complex with H3K9me3 peptide

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Navigation menu

Page actions

Page actions

Personal tools

Navigation

Search

Tools