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.

6irm

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 06:57, 17 April 2019

The crosslinked complex of ISWI-nucleosome in the ADP.BeF-bound state

Structural highlights

6irm is a 11 chain structure with sequence from [1], African clawed frog, Baker's yeast and Ecoli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Gene:	XELAEV_18002543mg (African clawed frog), hist1h2aj, LOC494591, XELAEV_18003602mg (African clawed frog), ISW1, YBR245C, YBR1633 (Baker's yeast)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[H2B11_XENLA] Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling. [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] [H4_XENLA] Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling.

Publication Abstract from PubMed

Chromatin remodelers are diverse enzymes, and different models have been proposed to explain how these proteins work. Here we report the 3.3 A-resolution cryogenic electron microscopy (cryo-EM) structures of Saccharomyces cerevisiae ISWI (ISW1) in complex with the nucleosome in adenosine diphosphate (ADP)-bound and ADP-BeFx-bound states. The data show that after nucleosome binding, ISW1 is activated by substantial rearrangement of the catalytic domains, with the regulatory AutoN domain packing the first RecA-like core and the NegC domain being disordered. The high-resolution structure reveals local DNA distortion and translocation induced by ISW1 in the ADP-bound state, which is essentially identical to that induced by the Snf2 chromatin remodeler, suggesting a common mechanism of DNA translocation. The histone core remains largely unperturbed, and prevention of histone distortion by crosslinking did not inhibit the activity of yeast ISW1 or its human homolog. Together, our findings suggest a general mechanism of chromatin remodeling involving local DNA distortion without notable histone deformation.

Structures of the ISWI-nucleosome complex reveal a conserved mechanism of chromatin remodeling.,Yan L, Wu H, Li X, Gao N, Chen Z Nat Struct Mol Biol. 2019 Mar 13. pii: 10.1038/s41594-019-0199-9. doi:, 10.1038/s41594-019-0199-9. PMID:30872815^[5]

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

References

↑ 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
↑ 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
↑ 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
↑ 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
↑ Yan L, Wu H, Li X, Gao N, Chen Z. Structures of the ISWI-nucleosome complex reveal a conserved mechanism of chromatin remodeling. Nat Struct Mol Biol. 2019 Mar 13. pii: 10.1038/s41594-019-0199-9. doi:, 10.1038/s41594-019-0199-9. PMID:30872815 doi:http://dx.doi.org/10.1038/s41594-019-0199-9

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/6irm"

@@ Line 3: / Line 3: @@
 <StructureSection load='6irm' size='340' side='right'caption='[[6irm]], [[Resolution|resolution]] 3.37&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6irm]] is a 11 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IRM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6IRM FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6irm]] is a 11 chain structure with sequence from [http://en.wikipedia.org/wiki/ ], [http://en.wikipedia.org/wiki/African_clawed_frog African clawed frog], [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast] and [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IRM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6IRM FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene></td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">XELAEV_18002543mg ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=8355 African clawed frog]), hist1h2aj, LOC494591, XELAEV_18003602mg ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=8355 African clawed frog]), ISW1, YBR245C, YBR1633 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</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=6irm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6irm OCA], [http://pdbe.org/6irm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6irm RCSB], [http://www.ebi.ac.uk/pdbsum/6irm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6irm ProSAT]</span></td></tr>
 </table>
@@ Line 22: / Line 23: @@
 __TOC__
 </StructureSection>
+[[Category: African clawed frog]]
+[[Category: Baker's yeast]]
+[[Category: Ecoli]]
 [[Category: Large Structures]]
 [[Category: Chen, Z C]]

6irm

From Proteopedia

Revision as of 06:57, 17 April 2019

The crosslinked complex of ISWI-nucleosome in the ADP.BeF-bound state

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox