6gen: Difference between revisions
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The | ==Chromatin remodeller-nucleosome complex at 4.5 A resolution.== | ||
<SX load='6gen' size='340' side='right' viewer='molstar' caption='[[6gen]], [[Resolution|resolution]] 3.60Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[6gen]] is a 20 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] 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=6GEN OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6GEN 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>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | |||
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr> | |||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[6gej|6gej]]</td></tr> | |||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">VPS71, SWC6, YML041C, YM8054.02C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), RVB1, TIH1, TIP49A, YDR190C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), RVB2, TIH2, TIP49B, YPL235W, P1060 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), HHT1, YBR010W, YBR0201, HHT2, SIN2, YNL031C, N2749 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), HHF1, YBR009C, YBR0122, HHF2, YNL030W, N2752 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), HTA1, H2A1, SPT11, YDR225W, YD9934.10 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), HTB1, H2B1, SPT12, YDR224C, YD9934.09C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), SWR1, YDR334W, D9651.6 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), ARP6, YLR085C, L2393, L9449.13 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</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'>[http://proteopedia.org/fgij/fg.htm?mol=6gen FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6gen OCA], [http://pdbe.org/6gen PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6gen RCSB], [http://www.ebi.ac.uk/pdbsum/6gen PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6gen ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[[http://www.uniprot.org/uniprot/RUVB1_YEAST RUVB1_YEAST]] DNA helicase which participates in several chromatin remodeling complexes, including the SWR1 and the INO80 complexes. The SWR1 complex mediates the ATP-dependent exchange of histone H2A for the H2A variant HZT1 leading to transcriptional regulation of selected genes by chromatin remodeling. The INO80 complex 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 'Ser-129' phosphorylated H2A histones as a response to DNA damage. RVB1 recruits ARP5 to the INO80 complex. During transcription may recruit SPT15/TBP to the TATA-boxes of involved genes. Required for box C/D and box H/ACA snoRNA accumulation and involved in pre-rRNA processing.<ref>PMID:10952318</ref> <ref>PMID:11278922</ref> <ref>PMID:14645854</ref> <ref>PMID:14690608</ref> <ref>PMID:15045029</ref> <ref>PMID:15525518</ref> [[http://www.uniprot.org/uniprot/ARP6_YEAST ARP6_YEAST]] 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. Involved in chromosome stability.<ref>PMID:14645854</ref> <ref>PMID:14690608</ref> <ref>PMID:15045029</ref> [[http://www.uniprot.org/uniprot/RUVB2_YEAST RUVB2_YEAST]] DNA helicase which participates in several chromatin remodeling complexes, including the SWR1 and the INO80 complexes. The SWR1 complex mediates the ATP-dependent exchange of histone H2A for the H2A variant HZT1 leading to transcriptional regulation of selected genes by chromatin remodeling. The INO80 complex 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 'Ser-129' phosphorylated H2A histones as a response to DNA damage. During transcription may recruit SPT15/TBP to the TATA-boxes of involved genes. Required for box C/D and box H/ACA snoRNA accumulation and involved in pre-rRNA processing.<ref>PMID:10787406</ref> <ref>PMID:10952318</ref> <ref>PMID:11278922</ref> <ref>PMID:11604509</ref> <ref>PMID:12576485</ref> <ref>PMID:14645854</ref> <ref>PMID:14690608</ref> <ref>PMID:15045029</ref> <ref>PMID:15525518</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/H2A1_YEAST H2A1_YEAST]] Core component of nucleosome which plays a central role in DNA double strand break (DSB) repair. 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.<ref>PMID:11140636</ref> <ref>PMID:15458641</ref> <ref>PMID:15610741</ref> <ref>PMID:16299494</ref> [[http://www.uniprot.org/uniprot/VPS71_YEAST VPS71_YEAST]] Participates in the catalytic exchange of histone H2A for the H2A variant HZT1, an euchromatin-specific factor, leading to chromatin remodeling and changes in transcription of targeted genes. Indirectly involved in vacuolar protein sorting.<ref>PMID:12134085</ref> <ref>PMID:14645854</ref> <ref>PMID:14690608</ref> <ref>PMID:15045029</ref> [[http://www.uniprot.org/uniprot/H2B1_YEAST H2B1_YEAST]] 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.<ref>PMID:11973294</ref> <ref>PMID:12152067</ref> <ref>PMID:14752010</ref> <ref>PMID:15280549</ref> <ref>PMID:15652479</ref> <ref>PMID:15970663</ref> <ref>PMID:15632126</ref> <ref>PMID:15632065</ref> <ref>PMID:16598039</ref> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
The yeast SWR1 complex exchanges histone H2A in nucleosomes with Htz1 (H2A.Z in humans). The cryo-electron microscopy structure of the SWR1 complex bound to a nucleosome at 3.6-angstrom resolution reveals details of the intricate interactions between components of the SWR1 complex and its nucleosome substrate. Interactions between the Swr1 motor domains and the DNA wrap at superhelical location 2 distort the DNA, causing a bulge with concomitant translocation of the DNA by one base pair, coupled to conformational changes of the histone core. Furthermore, partial unwrapping of the DNA from the histone core takes place upon binding of nucleosomes to SWR1 complex. The unwrapping, as monitored by single-molecule data, is stabilized and has its dynamics altered by adenosine triphosphate binding but does not require hydrolysis. | |||
Structure and dynamics of the yeast SWR1-nucleosome complex.,Willhoft O, Ghoneim M, Lin CL, Chua EYD, Wilkinson M, Chaban Y, Ayala R, McCormack EA, Ocloo L, Rueda DS, Wigley DB Science. 2018 Oct 12;362(6411). pii: 362/6411/eaat7716. doi:, 10.1126/science.aat7716. PMID:30309918<ref>PMID:30309918</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
<div class="pdbe-citations 6gen" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Helicase 3D structures|Helicase 3D structures]] | |||
*[[Histone 3D structures|Histone 3D structures]] | |||
*[[Vacuolar protein sorting-associated protein 3D structures|Vacuolar protein sorting-associated protein 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</SX> | |||
[[Category: Baker's yeast]] | |||
[[Category: DNA helicase]] | |||
[[Category: Large Structures]] | |||
[[Category: Chua, E Y.D]] | |||
[[Category: Wigley, D B]] | |||
[[Category: Wilkinson, M]] | [[Category: Wilkinson, M]] | ||
[[Category: Willhoft, O]] | [[Category: Willhoft, O]] | ||
[[Category: Atpase]] | |||
[[Category: Chromatin]] | |||
[[Category: Histone]] | |||
[[Category: Nuclear protein]] | |||
[[Category: Remodeller]] | |||