5i9e

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of a nuclear actin ternary complex

Structural highlights

5i9e is a 6 chain structure with sequence from Saccharomyces bayanus and Saccharomyces cerevisiae S288C. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.8Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

ARP4_YEAST Chromatin interaction component of the NuA4 histone acetyltransferase complex which is involved in transcriptional activation of selected genes principally by acetylation of nucleosomal histone H4 and H2A. The NuA4 complex is also involved in DNA repair. ARP4 recognizes H2AS128ph (gamma-H2A) and is required for NuA4 complex integrity. Component of the SWR1 complex which mediates the ATP-dependent exchange of histone H2A for the H2A variant HZT1 leading to transcriptional regulation of selected genes by chromatin remodeling. Component of the INO80 complex which remodels chromatin by shifting nucleosomes. Its ability to induce transcription of some phosphate-responsive genes is modulated by inositol polyphosphates. The INO80 complex is involved in DNA repair by associating to gamma-H2A as a response to DNA damage.^[1] ^[2] ^[3] ^[4] ^[5] ^[6] ^[7] ^[8] ^[9]

Publication Abstract from PubMed

Actin polymerizes and forms filamentous structures (F-actin) in the cytoplasm of eukaryotic cells. It also exists in the nucleus and regulates various nucleic acid transactions, particularly through its incorporation into multiple chromatin-remodeling complexes. However, the specific structure of actin and the mechanisms that regulate its polymeric nature inside the nucleus remain unknown. Here, we report the crystal structure of nuclear actin (N-actin) complexed with actin-related protein 4 (Arp4) and the helicase-SANT-associated (HSA) domain of the chromatin remodeler Swr1. The inner face and barbed end of N-actin are sequestered by interactions with Arp4 and the HSA domain, respectively, which prevents N-actin from polymerization and binding to many actin regulators. The two major domains of N-actin are more twisted than those of globular actin (G-actin), and its nucleotide-binding pocket is occluded, freeing N-actin from binding to and regulation by ATP. These findings revealed the salient structural features of N-actin that distinguish it from its cytoplasmic counterpart and provide a rational basis for its functions and regulation inside the nucleus.

Crystal structure of a nuclear actin ternary complex.,Cao T, Sun L, Jiang Y, Huang S, Wang J, Chen Z Proc Natl Acad Sci U S A. 2016 Aug 9;113(32):8985-90. doi:, 10.1073/pnas.1602818113. Epub 2016 Jul 25. PMID:27457955^[10]

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

References

↑ Galarneau L, Nourani A, Boudreault AA, Zhang Y, Heliot L, Allard S, Savard J, Lane WS, Stillman DJ, Cote J. Multiple links between the NuA4 histone acetyltransferase complex and epigenetic control of transcription. Mol Cell. 2000 Jun;5(6):927-37. PMID:10911987
↑ Shen X, Mizuguchi G, Hamiche A, Wu C. A chromatin remodelling complex involved in transcription and DNA processing. Nature. 2000 Aug 3;406(6795):541-4. PMID:10952318 doi:http://dx.doi.org/10.1038/35020123
↑ Harata M, Zhang Y, Stillman DJ, Matsui D, Oma Y, Nishimori K, Mochizuki R. Correlation between chromatin association and transcriptional regulation for the Act3p/Arp4 nuclear actin-related protein of Saccharomyces cerevisiae. Nucleic Acids Res. 2002 Apr 15;30(8):1743-50. PMID:11937627
↑ Bird AW, Yu DY, Pray-Grant MG, Qiu Q, Harmon KE, Megee PC, Grant PA, Smith MM, Christman MF. Acetylation of histone H4 by Esa1 is required for DNA double-strand break repair. Nature. 2002 Sep 26;419(6905):411-5. PMID:12353039 doi:http://dx.doi.org/10.1038/nature01035
↑ Gorzer I, Schuller C, Heidenreich E, Krupanska L, Kuchler K, Wintersberger U. The nuclear actin-related protein Act3p/Arp4p of Saccharomyces cerevisiae is involved in transcription regulation of stress genes. Mol Microbiol. 2003 Nov;50(4):1155-71. PMID:14622406
↑ Mizuguchi G, Shen X, Landry J, Wu WH, Sen S, Wu C. ATP-driven exchange of histone H2AZ variant catalyzed by SWR1 chromatin remodeling complex. Science. 2004 Jan 16;303(5656):343-8. Epub 2003 Nov 26. PMID:14645854 doi:10.1126/science.1090701
↑ Krogan NJ, Keogh MC, Datta N, Sawa C, Ryan OW, Ding H, Haw RA, Pootoolal J, Tong A, Canadien V, Richards DP, Wu X, Emili A, Hughes TR, Buratowski S, Greenblatt JF. A Snf2 family ATPase complex required for recruitment of the histone H2A variant Htz1. Mol Cell. 2003 Dec;12(6):1565-76. PMID:14690608
↑ Kobor MS, Venkatasubrahmanyam S, Meneghini MD, Gin JW, Jennings JL, Link AJ, Madhani HD, Rine J. A protein complex containing the conserved Swi2/Snf2-related ATPase Swr1p deposits histone variant H2A.Z into euchromatin. PLoS Biol. 2004 May;2(5):E131. Epub 2004 Mar 23. PMID:15045029 doi:10.1371/journal.pbio.0020131
↑ Downs JA, Allard S, Jobin-Robitaille O, Javaheri A, Auger A, Bouchard N, Kron SJ, Jackson SP, Cote J. Binding of chromatin-modifying activities to phosphorylated histone H2A at DNA damage sites. Mol Cell. 2004 Dec 22;16(6):979-90. PMID:15610740 doi:http://dx.doi.org/S1097276504007580
↑ Cao T, Sun L, Jiang Y, Huang S, Wang J, Chen Z. Crystal structure of a nuclear actin ternary complex. Proc Natl Acad Sci U S A. 2016 Aug 9;113(32):8985-90. doi:, 10.1073/pnas.1602818113. Epub 2016 Jul 25. PMID:27457955 doi:http://dx.doi.org/10.1073/pnas.1602818113

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/5i9e"

Categories: Large Structures | Saccharomyces bayanus | Saccharomyces cerevisiae S288C | Cao T | Chen Z

@@ Line 3: / Line 3: @@
 <StructureSection load='5i9e' size='340' side='right'caption='[[5i9e]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5i9e]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast] and [http://en.wikipedia.org/wiki/Cbs_380 Cbs 380]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5I9E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5I9E FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5i9e]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_bayanus Saccharomyces bayanus] and [https://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=5I9E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5I9E FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</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">X-ray diffraction, [[Resolution|Resolution]] 2.8&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ARP4, ACT3, YJL081C, J1012 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), ACT1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4931 CBS 380]), SWR1, YDR334W, D9651.6 ([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=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/DNA_helicase DNA helicase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.4.12 3.6.4.12] </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=5i9e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i9e OCA], [https://pdbe.org/5i9e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5i9e RCSB], [https://www.ebi.ac.uk/pdbsum/5i9e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5i9e ProSAT]</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=5i9e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5i9e OCA], [http://pdbe.org/5i9e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5i9e RCSB], [http://www.ebi.ac.uk/pdbsum/5i9e PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5i9e ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/ARP4_YEAST ARP4_YEAST]] Chromatin interaction component of the NuA4 histone acetyltransferase complex which is involved in transcriptional activation of selected genes principally by acetylation of nucleosomal histone H4 and H2A. The NuA4 complex is also involved in DNA repair. ARP4 recognizes H2AS128ph (gamma-H2A) and is required for NuA4 complex integrity. Component of the SWR1 complex which mediates the ATP-dependent exchange of histone H2A for the H2A variant HZT1 leading to transcriptional regulation of selected genes by chromatin remodeling. Component of the INO80 complex which remodels chromatin by shifting nucleosomes. Its ability to induce transcription of some phosphate-responsive genes is modulated by inositol polyphosphates. The INO80 complex is involved in DNA repair by associating to gamma-H2A as a response to DNA damage.<ref>PMID:10911987</ref> <ref>PMID:10952318</ref> <ref>PMID:11937627</ref> <ref>PMID:12353039</ref> <ref>PMID:14622406</ref> <ref>PMID:14645854</ref> <ref>PMID:14690608</ref> <ref>PMID:15045029</ref> <ref>PMID:15610740</ref>  [[http://www.uniprot.org/uniprot/SWR1_YEAST SWR1_YEAST]] Catalytic component of the SWR1 complex which mediates the ATP-dependent exchange of histone H2A for the H2A variant HZT1 leading to transcriptional regulation of selected genes by chromatin remodeling.<ref>PMID:14690608</ref> <ref>PMID:15045029</ref> <ref>PMID:15353583</ref> <ref>PMID:14645854</ref>  [[http://www.uniprot.org/uniprot/ACT_SACBA ACT_SACBA]] Actins are highly conserved proteins that are involved in various types of cell motility and are ubiquitously expressed in all eukaryotic cells.
+[https://www.uniprot.org/uniprot/ARP4_YEAST ARP4_YEAST] Chromatin interaction component of the NuA4 histone acetyltransferase complex which is involved in transcriptional activation of selected genes principally by acetylation of nucleosomal histone H4 and H2A. The NuA4 complex is also involved in DNA repair. ARP4 recognizes H2AS128ph (gamma-H2A) and is required for NuA4 complex integrity. Component of the SWR1 complex which mediates the ATP-dependent exchange of histone H2A for the H2A variant HZT1 leading to transcriptional regulation of selected genes by chromatin remodeling. Component of the INO80 complex which remodels chromatin by shifting nucleosomes. Its ability to induce transcription of some phosphate-responsive genes is modulated by inositol polyphosphates. The INO80 complex is involved in DNA repair by associating to gamma-H2A as a response to DNA damage.<ref>PMID:10911987</ref> <ref>PMID:10952318</ref> <ref>PMID:11937627</ref> <ref>PMID:12353039</ref> <ref>PMID:14622406</ref> <ref>PMID:14645854</ref> <ref>PMID:14690608</ref> <ref>PMID:15045029</ref> <ref>PMID:15610740</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 23: / Line 22: @@
 ==See Also==
 *[[Actin 3D structures|Actin 3D structures]]
+*[[Actin-related protein 3D structures|Actin-related protein 3D structures]]
 *[[Helicase 3D structures|Helicase 3D structures]]
 == References ==
@@ Line 28: / Line 28: @@
 __TOC__
 </StructureSection>
-[[Category: Baker's yeast]]
-[[Category: Cbs 380]]
-[[Category: DNA helicase]]
 [[Category: Large Structures]]
-[[Category: Cao, T]]
+[[Category: Saccharomyces bayanus]]
-[[Category: Chen, Z]]
+[[Category: Saccharomyces cerevisiae S288C]]
-[[Category: Arp4]]
+[[Category: Cao T]]
-[[Category: Chromatin remodeling]]
+[[Category: Chen Z]]
-[[Category: Hydrolase]]
-[[Category: Nuclear actin]]

5i9e

From Proteopedia

Current revision

Crystal structure of a nuclear actin ternary complex

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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