5z3l: Difference between revisions

Latest revision as of 05:43, 3 July 2025

Structure of Snf2-nucleosome complex in apo state

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Structural highlights

5z3l is a 11 chain structure with sequence from Saccharomyces cerevisiae S288C, Xenopus laevis and Synthetic construct. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Electron Microscopy, Resolution 4.31Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Publication Abstract from PubMed

Chromatin remodellers include diverse enzymes with distinct biological functions, but nucleosome-sliding activity appears to be a common theme(1,2). Among the remodelling enzymes, Snf2 serves as the prototype to study the action of this protein family. Snf2 and related enzymes share two conserved RecA-like lobes(3), which by themselves are able to couple ATP hydrolysis to chromatin remodelling. The mechanism by which these enzymes couple ATP hydrolysis to translocate the nucleosome along the DNA remains unclear(2,4-8). Here we report the structures of Saccharomyces cerevisiae Snf2 bound to the nucleosome in the presence of ADP and ADP-BeFx. Snf2 in the ADP-bound state adopts an open conformation similar to that in the apo state, and induces a one-base-pair DNA bulge at superhelix location 2 (SHL2), with the tracking strand showing greater distortion than the guide strand. The DNA distortion propagates to the proximal end, leading to staggered translocation of the two strands. The binding of ADP-BeFx triggers a closed conformation of the enzyme, resetting the nucleosome to a relaxed state. Snf2 shows altered interactions with the DNA in different nucleotide states, providing the structural basis for DNA translocation. Together, our findings suggest a fundamental mechanism for the DNA translocation that underlies chromatin remodelling.

Mechanism of DNA translocation underlying chromatin remodelling by Snf2.,Li M, Xia X, Tian Y, Jia Q, Liu X, Lu Y, Li M, Li X, Chen Z Nature. 2019 Mar;567(7748):409-413. doi: 10.1038/s41586-019-1029-2. Epub 2019 Mar, 13. PMID:30867599^[1]

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

References

↑ Li M, Xia X, Tian Y, Jia Q, Liu X, Lu Y, Li M, Li X, Chen Z. Mechanism of DNA translocation underlying chromatin remodelling by Snf2. Nature. 2019 Mar;567(7748):409-413. doi: 10.1038/s41586-019-1029-2. Epub 2019 Mar, 13. PMID:30867599 doi:https://dx.doi.org/10.1038/s41586-019-1029-2

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OCA

[1] Li M, Xia X, Tian Y, Jia Q, Liu X, Lu Y, Li M, Li X, Chen Z. Mechanism of DNA translocation underlying chromatin remodelling by Snf2. Nature. 2019 Mar;567(7748):409-413. doi: 10.1038/s41586-019-1029-2. Epub 2019 Mar, 13. PMID:30867599 doi:https://dx.doi.org/10.1038/s41586-019-1029-2

[1]

@@ Line 3: / Line 3: @@
 <SX load='5z3l' size='340' side='right' viewer='molstar' caption='[[5z3l]], [[Resolution|resolution]] 4.31&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5z3l]] is a 11 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z3L OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5Z3L FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5z3l]] is a 11 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C], [https://en.wikipedia.org/wiki/Xenopus_laevis Xenopus laevis] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z3L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5Z3L FirstGlance]. <br>
-</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=5z3l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z3l OCA], [http://pdbe.org/5z3l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5z3l RCSB], [http://www.ebi.ac.uk/pdbsum/5z3l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5z3l ProSAT]</span></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]] 4.31&#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=5z3l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z3l OCA], [https://pdbe.org/5z3l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5z3l RCSB], [https://www.ebi.ac.uk/pdbsum/5z3l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5z3l 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/H32_XENLA H32_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/SNF2_YEAST SNF2_YEAST]] Involved in transcriptional activation. Catalytic component of the SWI/SNF complex, an ATP-dependent chromatin-remodeling complex, which is required for the positive and negative regulation of gene expression of a large number of genes. It changes chromatin structure by altering DNA-histone contacts within a nucleosome, leading eventually to a change in nucleosome position, thus facilitating or repressing binding of gene-specific transcription factors. [[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.
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 25: / Line 24: @@
 </SX>
 [[Category: Large Structures]]
-[[Category: Chen, Z]]
+[[Category: Saccharomyces cerevisiae S288C]]
-[[Category: Li, M]]
+[[Category: Synthetic construct]]
-[[Category: Li, X]]
+[[Category: Xenopus laevis]]
-[[Category: Liu, X]]
+[[Category: Chen Z]]
-[[Category: Xia, X]]
+[[Category: Li M]]
-[[Category: Chromatin remodeling]]
+[[Category: Li X]]
-[[Category: Complex]]
+[[Category: Liu X]]
-[[Category: Gene regulation]]
+[[Category: Xia X]]
-[[Category: Nucleosome]]
-[[Category: Structural protein-hydrolase-dna complex]]

5z3l: Difference between revisions

Latest revision as of 05:43, 3 July 2025

Structure of Snf2-nucleosome complex in apo state

Structural highlights

Publication Abstract from PubMed

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References

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