6jyl: Difference between revisions

Latest revision as of 13:20, 13 August 2026

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

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Structural highlights

6jyl is a 11 chain structure with sequence from Escherichia coli K-12, Saccharomyces cerevisiae S288C and Xenopus laevis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Electron Microscopy, Resolution 3.37Å
Ligands:	ADP, BEF, MG
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

A0A310TTQ1_XENLA

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^[1]

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

References

↑ 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:https://dx.doi.org/10.1038/s41594-019-0199-9

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] 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:https://dx.doi.org/10.1038/s41594-019-0199-9

[1]

@@ Line 3: / Line 3: @@
 <SX load='6jyl' size='340' side='right' viewer='molstar' caption='[[6jyl]], [[Resolution|resolution]] 3.37&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6jyl]] is a 11 chain structure with sequence from [http://en.wikipedia.org/wiki/ ], [http://en.wikipedia.org/wiki/African_clawed_frog African clawed frog] and [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=6irm 6irm]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JYL OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6JYL FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6jyl]] is a 11 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12], [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C] and [https://en.wikipedia.org/wiki/Xenopus_laevis Xenopus laevis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JYL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6JYL FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.37&#8491;</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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=BEF:BERYLLIUM+TRIFLUORIDE+ION'>BEF</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6jyl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jyl OCA], [http://pdbe.org/6jyl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jyl RCSB], [http://www.ebi.ac.uk/pdbsum/6jyl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jyl ProSAT]</span></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=6jyl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jyl OCA], [https://pdbe.org/6jyl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6jyl RCSB], [https://www.ebi.ac.uk/pdbsum/6jyl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6jyl ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/H2B11_XENLA 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. [[http://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>  [[http://www.uniprot.org/uniprot/H4_XENLA 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.
+[https://www.uniprot.org/uniprot/A0A310TTQ1_XENLA A0A310TTQ1_XENLA]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 26: / Line 26: @@
 __TOC__
 </SX>
-[[Category: African clawed frog]]
+[[Category: Escherichia coli K-12]]
-[[Category: Baker's yeast]]
 [[Category: Large Structures]]
-[[Category: Chen, Z C]]
+[[Category: Saccharomyces cerevisiae S288C]]
-[[Category: Gao, N]]
+[[Category: Xenopus laevis]]
-[[Category: Li, X M]]
+[[Category: Chen ZC]]
-[[Category: Wu, H]]
+[[Category: Gao N]]
-[[Category: Yan, L J]]
+[[Category: Li XM]]
-[[Category: Chromatin remodelling]]
+[[Category: Wu H]]
-[[Category: Dna binding protein-dna complex]]
+[[Category: Yan LJ]]
-[[Category: Nucleosome]]
-[[Category: Single particle cryo-em]]

6jyl: Difference between revisions

Latest revision as of 13:20, 13 August 2026

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

Structural highlights

Function

Publication Abstract from PubMed

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References

Contents

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