2y9y: Difference between revisions

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'''Unreleased structure'''


The entry 2y9y is ON HOLD  until Paper Publication
==Chromatin Remodeling Factor ISW1a(del_ATPase)==
<StructureSection load='2y9y' size='340' side='right'caption='[[2y9y]], [[Resolution|resolution]] 3.25&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2y9y]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Y9Y OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Y9Y 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]] 3.25&#8491;</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=2y9y FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2y9y OCA], [https://pdbe.org/2y9y PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2y9y RCSB], [https://www.ebi.ac.uk/pdbsum/2y9y PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2y9y ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/ISW1_YEAST ISW1_YEAST] Catalytic component of ISW1-type complexes, which act by remodeling the chromatin by catalyzing an ATP-dependent alteration in the structure of nucleosomal DNA. They are involved in coordinating transcriptional repression, activation and elongation phases. The ISW1A complex represses gene expression at initiation through specific positioning of a promoter proximal dinucleosome. The ISW1B complex acts within coding regions to control the amount of RNA polymerase II released into productive elongation and to coordinate elongation with termination and pre-mRNA processing.<ref>PMID:10090725</ref> <ref>PMID:11238381</ref> <ref>PMID:14622597</ref> <ref>PMID:12482963</ref>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Site-specific recognition of DNA in eukaryotic organisms depends on the arrangement of nucleosomes in chromatin. In the yeast Saccharomyces cerevisiae, ISW1a and related chromatin remodelling factors are implicated in establishing the nucleosome repeat during replication and altering nucleosome position to affect gene activity. Here we have solved the crystal structures of S. cerevisiae ISW1a lacking its ATPase domain both alone and with DNA bound at resolutions of 3.25 A and 3.60 A, respectively, and we have visualized two different nucleosome-containing remodelling complexes using cryo-electron microscopy. The composite X-ray and electron microscopy structures combined with site-directed photocrosslinking analyses of these complexes suggest that ISW1a uses a dinucleosome substrate for chromatin remodelling. Results from a remodelling assay corroborate the dinucleosome model. We show how a chromatin remodelling factor could set the spacing between two adjacent nucleosomes acting as a 'protein ruler'.


Authors: Yamada, K., Frouws, T.D., Angst, B., Fitzgerald, D.J., DeLuca, C., Schimmele, K., Sargent, D.F., Richmond, T.J.
Structure and mechanism of the chromatin remodelling factor ISW1a.,Yamada K, Frouws TD, Angst B, Fitzgerald DJ, DeLuca C, Schimmele K, Sargent DF, Richmond TJ Nature. 2011 Apr 28;472(7344):448-53. PMID:21525927<ref>PMID:21525927</ref>


Description: Chromatin Remodeling Factor ISW1a(del_ATPase)
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2y9y" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Angst B]]
[[Category: DeLuca C]]
[[Category: Fitzgerald DJ]]
[[Category: Frouws TD]]
[[Category: Richmond TJ]]
[[Category: Sargent DF]]
[[Category: Schimmele K]]
[[Category: Yamada K]]

Latest revision as of 17:03, 1 February 2024

Chromatin Remodeling Factor ISW1a(del_ATPase)Chromatin Remodeling Factor ISW1a(del_ATPase)

Structural highlights

2y9y is a 2 chain structure with sequence from Saccharomyces cerevisiae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 3.25Å
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

ISW1_YEAST Catalytic component of ISW1-type complexes, which act by remodeling the chromatin by catalyzing an ATP-dependent alteration in the structure of nucleosomal DNA. They are involved in coordinating transcriptional repression, activation and elongation phases. The ISW1A complex represses gene expression at initiation through specific positioning of a promoter proximal dinucleosome. The ISW1B complex acts within coding regions to control the amount of RNA polymerase II released into productive elongation and to coordinate elongation with termination and pre-mRNA processing.[1] [2] [3] [4]

Publication Abstract from PubMed

Site-specific recognition of DNA in eukaryotic organisms depends on the arrangement of nucleosomes in chromatin. In the yeast Saccharomyces cerevisiae, ISW1a and related chromatin remodelling factors are implicated in establishing the nucleosome repeat during replication and altering nucleosome position to affect gene activity. Here we have solved the crystal structures of S. cerevisiae ISW1a lacking its ATPase domain both alone and with DNA bound at resolutions of 3.25 A and 3.60 A, respectively, and we have visualized two different nucleosome-containing remodelling complexes using cryo-electron microscopy. The composite X-ray and electron microscopy structures combined with site-directed photocrosslinking analyses of these complexes suggest that ISW1a uses a dinucleosome substrate for chromatin remodelling. Results from a remodelling assay corroborate the dinucleosome model. We show how a chromatin remodelling factor could set the spacing between two adjacent nucleosomes acting as a 'protein ruler'.

Structure and mechanism of the chromatin remodelling factor ISW1a.,Yamada K, Frouws TD, Angst B, Fitzgerald DJ, DeLuca C, Schimmele K, Sargent DF, Richmond TJ Nature. 2011 Apr 28;472(7344):448-53. PMID:21525927[5]

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

References

  1. ↑ Tsukiyama T, Palmer J, Landel CC, Shiloach J, Wu C. Characterization of the imitation switch subfamily of ATP-dependent chromatin-remodeling factors in Saccharomyces cerevisiae. Genes Dev. 1999 Mar 15;13(6):686-97. PMID:10090725
  2. ↑ Kent NA, Karabetsou N, Politis PK, Mellor J. In vivo chromatin remodeling by yeast ISWI homologs Isw1p and Isw2p. Genes Dev. 2001 Mar 1;15(5):619-26. PMID:11238381 doi:http://dx.doi.org/10.1101/gad.190301
  3. ↑ Morillon A, Karabetsou N, O'Sullivan J, Kent N, Proudfoot N, Mellor J. Isw1 chromatin remodeling ATPase coordinates transcription elongation and termination by RNA polymerase II. Cell. 2003 Nov 14;115(4):425-35. PMID:14622597
  4. ↑ Vary JC Jr, Gangaraju VK, Qin J, Landel CC, Kooperberg C, Bartholomew B, Tsukiyama T. Yeast Isw1p forms two separable complexes in vivo. Mol Cell Biol. 2003 Jan;23(1):80-91. PMID:12482963
  5. ↑ Yamada K, Frouws TD, Angst B, Fitzgerald DJ, DeLuca C, Schimmele K, Sargent DF, Richmond TJ. Structure and mechanism of the chromatin remodelling factor ISW1a. Nature. 2011 Apr 28;472(7344):448-53. PMID:21525927 doi:10.1038/nature09947

2y9y, resolution 3.25Å

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