5z3v

From Proteopedia

(Difference between revisions)

Revision as of 22:49, 10 April 2020

Structure of Snf2-nucleosome complex at shl-2 in ADP BeFx state

5z3v, resolution 4.22Å

Structural highlights

5z3v is a 11 chain structure with sequence from African clawed frog and Baker's yeast. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Gene:	SNF2, GAM1, RIC1, SWI2, TYE3, YOR290C (Baker's yeast), hist1h2aj, LOC494591 (African clawed frog)
Experimental data:	Check to display Experimental Data
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[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. [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. [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. [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.

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:http://dx.doi.org/10.1038/s41586-019-1029-2

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5z3v"

@@ Line 3: / Line 3: @@
 <SX load='5z3v' size='340' side='right' viewer='molstar' caption='[[5z3v]], [[Resolution|resolution]] 4.22&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5z3v]] is a 11 chain structure with sequence from [http://en.wikipedia.org/wiki/African_clawed_frog African clawed frog] and [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z3V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5Z3V FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5z3v]] is a 11 chain structure with sequence from [http://en.wikipedia.org/wiki/African_clawed_frog African clawed frog] and [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5Z3V OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5Z3V 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>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
+</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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SNF2, GAM1, RIC1, SWI2, TYE3, YOR290C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), hist1h2aj, LOC494591 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=8355 African clawed frog])</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=5z3v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z3v OCA], [http://pdbe.org/5z3v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5z3v RCSB], [http://www.ebi.ac.uk/pdbsum/5z3v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5z3v ProSAT]</span></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=5z3v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5z3v OCA], [http://pdbe.org/5z3v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5z3v RCSB], [http://www.ebi.ac.uk/pdbsum/5z3v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5z3v ProSAT]</span></td></tr>
 </table>
 == Function ==

5z3v

From Proteopedia

Revision as of 22:49, 10 April 2020

Structure of Snf2-nucleosome complex at shl-2 in ADP BeFx state

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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