4i6m

From Proteopedia

(Difference between revisions)

Revision as of 18:27, 11 August 2016

Structure of Arp7-Arp9-Snf2(HSA)-RTT102 subcomplex of SWI/SNF chromatin remodeler.

Structural highlights

4i6m is a 4 chain structure with sequence from Baker's yeast. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
NonStd Res:
Gene:	SNF2, SNF2/YOR290C, SWI2, TYE3, YOR290C, GAM1, HAF1 (Baker's yeast), ARP9, Arp9/YMR033W, SWP59, YM9973.07, YMR033W (Baker's yeast), SNF2, SNF2/YOR290C, SWI2, TYE3, YOR290C, GAM1, HAF1 (Baker's yeast), RTT102, RTT102/YGR275W, YGR275W; (Baker's yeast)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[RT102_YEAST] Probable component of the chromatin structure-remodeling complex (RSC) which is involved in transcription regulation and nucleosome positioning. RSC is responsible for the transfer of a histone octamer from a nucleosome core particle to naked DNA. The reaction requires ATP and involves an activated RSC-nucleosome intermediate. Remodeling reaction also involves DNA translocation, DNA twist and conformational change. As a reconfigurer of centromeric and flanking nucleosomes, RSC complex is required both for proper kinetochore function in chromosome segregation and, via a PKC1-dependent signaling pathway, for organization of the cellular cytoskeleton. Probable component of the SWI/SNF complex, an ATP-dependent chromatin-remodeling complex, 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. [ARP7_YEAST] Component of the chromatin structure remodeling complex (RSC), which is involved in transcription regulation and nucleosome positioning. RSC is responsible for the transfer of a histone octamer from a nucleosome core particle to naked DNA. The reaction requires ATP and involves an activated RSC-nucleosome intermediate. Remodeling reaction also involves DNA translocation, DNA twist and conformational change. As a reconfigurer of centromeric and flanking nucleosomes, RSC complex is required both for proper kinetochore function in chromosome segregation and, via a PKC1-dependent signaling pathway, for organization of the cellular cytoskeleton. This subunit is involved in transcriptional regulation. Heterodimer of ARP7 and ARP9 functions with HMG box proteins to facilitate proper chromatin architecture. Heterodimer formation is necessary for assembly into RSC complex. Part of the SWI/SNF complex, an ATP-dependent chromatin remodeling complex, 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.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] [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. [ARP9_YEAST] Component of the chromatin structure remodeling complex (RSC), which is involved in transcription regulation and nucleosome positioning. RSC is responsible for the transfer of a histone octamer from a nucleosome core particle to naked DNA. The reaction requires ATP and involves an activated RSC-nucleosome intermediate. Remodeling reaction also involves DNA translocation, DNA twist and conformational change. As a reconfigurer of centromeric and flanking nucleosomes, RSC complex is required both for proper kinetochore function in chromosome segregation and, via a PKC1-dependent signaling pathway, for organization of the cellular cytoskeleton. This subunit is involved in transcriptional regulation. Heterodimer of ARP9 and ARP7 functions with HMG box proteins to facilitate proper chromatin architecture. Heterodimer formation is necessary for assembly into RSC complex. Part of the SWI/SNF complex, an ATP-dependent chromatin remodeling complex, 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.^[9] ^[10] ^[11] ^[12] ^[13] ^[14] ^[15] ^[16]

Publication Abstract from PubMed

The packaging of DNA into nucleosomal structures limits access for templated processes such as transcription and DNA repair. The repositioning or ejection of nucleosomes is therefore critically important for regulated events, including gene expression. This activity is provided by chromatin remodeling complexes, or remodelers, which are typically large, multisubunit complexes that use an ATPase subunit to translocate the DNA. Many remodelers contain pairs or multimers of actin-related proteins (ARPs) that contact the helicase-SANT-associated (HSA) domain within the catalytic ATPase subunit and are thought to regulate ATPase activity. Here, we determined the structure of a four-protein subcomplex within the SWI/SNF remodeler that comprises the Snf2 HSA domain, Arp7, Arp9, and repressor of Ty1 transposition, gene 102 (Rtt102). Surprisingly, unlike characterized actin-actin associations, the two ARPs pack like spoons and straddle the HSA domain, which forms a 92-A-long helix. The ARP-HSA interactions are reminiscent of contacts between actin and many binding partners and are quite different from those in the Arp2/3 complex. Rtt102 wraps around one side of the complex in a highly extended conformation that contacts both ARPs and therefore stabilizes the complex, yet functions to reduce by approximately 2.4-fold the remodeling and ATPase activity of complexes containing the Snf2 ATPase domain. Thus, our structure provides a foundation for developing models of remodeler function, including mechanisms of coupling between ARPs and the ATPase translocation activity.

Structure of an actin-related subcomplex of the SWI/SNF chromatin remodeler.,Schubert HL, Wittmeyer J, Kasten MM, Hinata K, Rawling DC, Heroux A, Cairns BR, Hill CP Proc Natl Acad Sci U S A. 2013 Feb 26;110(9):3345-50. doi:, 10.1073/pnas.1215379110. Epub 2013 Feb 11. PMID:23401505^[17]

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

References

↑ Cairns BR, Erdjument-Bromage H, Tempst P, Winston F, Kornberg RD. Two actin-related proteins are shared functional components of the chromatin-remodeling complexes RSC and SWI/SNF. Mol Cell. 1998 Nov;2(5):639-51. PMID:9844636
↑ Cairns BR, Lorch Y, Li Y, Zhang M, Lacomis L, Erdjument-Bromage H, Tempst P, Du J, Laurent B, Kornberg RD. RSC, an essential, abundant chromatin-remodeling complex. Cell. 1996 Dec 27;87(7):1249-60. PMID:8980231
↑ Lorch Y, Zhang M, Kornberg RD. Histone octamer transfer by a chromatin-remodeling complex. Cell. 1999 Feb 5;96(3):389-92. PMID:10025404
↑ Moreira JM, Holmberg S. Transcriptional repression of the yeast CHA1 gene requires the chromatin-remodeling complex RSC. EMBO J. 1999 May 17;18(10):2836-44. PMID:10329629 doi:10.1093/emboj/18.10.2836
↑ Saha A, Wittmeyer J, Cairns BR. Chromatin remodeling by RSC involves ATP-dependent DNA translocation. Genes Dev. 2002 Aug 15;16(16):2120-34. PMID:12183366 doi:10.1101/gad.995002
↑ Chai B, Hsu JM, Du J, Laurent BC. Yeast RSC function is required for organization of the cellular cytoskeleton via an alternative PKC1 pathway. Genetics. 2002 Jun;161(2):575-84. PMID:12072455
↑ Szerlong H, Saha A, Cairns BR. The nuclear actin-related proteins Arp7 and Arp9: a dimeric module that cooperates with architectural proteins for chromatin remodeling. EMBO J. 2003 Jun 16;22(12):3175-87. PMID:12805231 doi:http://dx.doi.org/10.1093/emboj/cdg296
↑ Hsu JM, Huang J, Meluh PB, Laurent BC. The yeast RSC chromatin-remodeling complex is required for kinetochore function in chromosome segregation. Mol Cell Biol. 2003 May;23(9):3202-15. PMID:12697820
↑ Cairns BR, Erdjument-Bromage H, Tempst P, Winston F, Kornberg RD. Two actin-related proteins are shared functional components of the chromatin-remodeling complexes RSC and SWI/SNF. Mol Cell. 1998 Nov;2(5):639-51. PMID:9844636
↑ Cairns BR, Lorch Y, Li Y, Zhang M, Lacomis L, Erdjument-Bromage H, Tempst P, Du J, Laurent B, Kornberg RD. RSC, an essential, abundant chromatin-remodeling complex. Cell. 1996 Dec 27;87(7):1249-60. PMID:8980231
↑ Lorch Y, Zhang M, Kornberg RD. Histone octamer transfer by a chromatin-remodeling complex. Cell. 1999 Feb 5;96(3):389-92. PMID:10025404
↑ Moreira JM, Holmberg S. Transcriptional repression of the yeast CHA1 gene requires the chromatin-remodeling complex RSC. EMBO J. 1999 May 17;18(10):2836-44. PMID:10329629 doi:10.1093/emboj/18.10.2836
↑ Saha A, Wittmeyer J, Cairns BR. Chromatin remodeling by RSC involves ATP-dependent DNA translocation. Genes Dev. 2002 Aug 15;16(16):2120-34. PMID:12183366 doi:10.1101/gad.995002
↑ Chai B, Hsu JM, Du J, Laurent BC. Yeast RSC function is required for organization of the cellular cytoskeleton via an alternative PKC1 pathway. Genetics. 2002 Jun;161(2):575-84. PMID:12072455
↑ Szerlong H, Saha A, Cairns BR. The nuclear actin-related proteins Arp7 and Arp9: a dimeric module that cooperates with architectural proteins for chromatin remodeling. EMBO J. 2003 Jun 16;22(12):3175-87. PMID:12805231 doi:http://dx.doi.org/10.1093/emboj/cdg296
↑ Hsu JM, Huang J, Meluh PB, Laurent BC. The yeast RSC chromatin-remodeling complex is required for kinetochore function in chromosome segregation. Mol Cell Biol. 2003 May;23(9):3202-15. PMID:12697820
↑ Schubert HL, Wittmeyer J, Kasten MM, Hinata K, Rawling DC, Heroux A, Cairns BR, Hill CP. Structure of an actin-related subcomplex of the SWI/SNF chromatin remodeler. Proc Natl Acad Sci U S A. 2013 Feb 26;110(9):3345-50. doi:, 10.1073/pnas.1215379110. Epub 2013 Feb 11. PMID:23401505 doi:http://dx.doi.org/10.1073/pnas.1215379110

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/4i6m"

@@ Line 1: / Line 1: @@
 ==Structure of Arp7-Arp9-Snf2(HSA)-RTT102 subcomplex of SWI/SNF chromatin remodeler.==
 <StructureSection load='4i6m' size='340' side='right' caption='[[4i6m]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4i6m]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_s288c Saccharomyces cerevisiae s288c]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4I6M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4I6M FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4i6m]] is a 4 chain structure with sequence from [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=4I6M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4I6M FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
 <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SNF2, SNF2/YOR290C, SWI2, TYE3, YOR290C, GAM1, HAF1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Saccharomyces cerevisiae S288c]), ARP9, Arp9/YMR033W, SWP59, YM9973.07, YMR033W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Saccharomyces cerevisiae S288c]), SNF2, SNF2/YOR290C, SWI2, TYE3,  YOR290C, GAM1, HAF1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Saccharomyces cerevisiae S288c]), RTT102, RTT102/YGR275W, YGR275W; ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Saccharomyces cerevisiae S288c])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">SNF2, SNF2/YOR290C, SWI2, TYE3, YOR290C, GAM1, HAF1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), ARP9, Arp9/YMR033W, SWP59, YM9973.07, YMR033W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), SNF2, SNF2/YOR290C, SWI2, TYE3,  YOR290C, GAM1, HAF1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), RTT102, RTT102/YGR275W, YGR275W; ([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=4i6m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i6m OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4i6m RCSB], [http://www.ebi.ac.uk/pdbsum/4i6m PDBsum]</span></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=4i6m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4i6m OCA], [http://pdbe.org/4i6m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4i6m RCSB], [http://www.ebi.ac.uk/pdbsum/4i6m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4i6m ProSAT]</span></td></tr>
 </table>
+== Function ==
+[[http://www.uniprot.org/uniprot/RT102_YEAST RT102_YEAST]] Probable component of the chromatin structure-remodeling complex (RSC) which is involved in transcription regulation and nucleosome positioning. RSC is responsible for the transfer of a histone octamer from a nucleosome core particle to naked DNA. The reaction requires ATP and involves an activated RSC-nucleosome intermediate. Remodeling reaction also involves DNA translocation, DNA twist and conformational change. As a reconfigurer of centromeric and flanking nucleosomes, RSC complex is required both for proper kinetochore function in chromosome segregation and, via a PKC1-dependent signaling pathway, for organization of the cellular cytoskeleton. Probable component of the SWI/SNF complex, an ATP-dependent chromatin-remodeling complex, 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/ARP7_YEAST ARP7_YEAST]] Component of the chromatin structure remodeling complex (RSC), which is involved in transcription regulation and nucleosome positioning. RSC is responsible for the transfer of a histone octamer from a nucleosome core particle to naked DNA. The reaction requires ATP and involves an activated RSC-nucleosome intermediate. Remodeling reaction also involves DNA translocation, DNA twist and conformational change. As a reconfigurer of centromeric and flanking nucleosomes, RSC complex is required both for proper kinetochore function in chromosome segregation and, via a PKC1-dependent signaling pathway, for organization of the cellular cytoskeleton. This subunit is involved in transcriptional regulation. Heterodimer of ARP7 and ARP9 functions with HMG box proteins to facilitate proper chromatin architecture. Heterodimer formation is necessary for assembly into RSC complex. Part of the SWI/SNF complex, an ATP-dependent chromatin remodeling complex, 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.<ref>PMID:9844636</ref> <ref>PMID:8980231</ref> <ref>PMID:10025404</ref> <ref>PMID:10329629</ref> <ref>PMID:12183366</ref> <ref>PMID:12072455</ref> <ref>PMID:12805231</ref> <ref>PMID:12697820</ref>  [[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/ARP9_YEAST ARP9_YEAST]] Component of the chromatin structure remodeling complex (RSC), which is involved in transcription regulation and nucleosome positioning. RSC is responsible for the transfer of a histone octamer from a nucleosome core particle to naked DNA. The reaction requires ATP and involves an activated RSC-nucleosome intermediate. Remodeling reaction also involves DNA translocation, DNA twist and conformational change. As a reconfigurer of centromeric and flanking nucleosomes, RSC complex is required both for proper kinetochore function in chromosome segregation and, via a PKC1-dependent signaling pathway, for organization of the cellular cytoskeleton. This subunit is involved in transcriptional regulation. Heterodimer of ARP9 and ARP7 functions with HMG box proteins to facilitate proper chromatin architecture. Heterodimer formation is necessary for assembly into RSC complex. Part of the SWI/SNF complex, an ATP-dependent chromatin remodeling complex, 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.<ref>PMID:9844636</ref> <ref>PMID:8980231</ref> <ref>PMID:10025404</ref> <ref>PMID:10329629</ref> <ref>PMID:12183366</ref> <ref>PMID:12072455</ref> <ref>PMID:12805231</ref> <ref>PMID:12697820</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 16: / Line 19: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 4i6m" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Saccharomyces cerevisiae s288c]]
+[[Category: Baker's yeast]]
 [[Category: Cairns, B R]]
 [[Category: Hill, C P]]

4i6m

From Proteopedia

Revision as of 18:27, 11 August 2016

Structure of Arp7-Arp9-Snf2(HSA)-RTT102 subcomplex of SWI/SNF chromatin remodeler.

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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