6ftx

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==Structure of the chromatin remodelling enzyme Chd1 bound to a ubiquitinylated nucleosome==
==Structure of the chromatin remodelling enzyme Chd1 bound to a ubiquitinylated nucleosome==
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<StructureSection load='6ftx' size='340' side='right' caption='[[6ftx]], [[Resolution|resolution]] 4.50&Aring;' scene=''>
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<SX load='6ftx' size='340' side='right' viewer='molstar' caption='[[6ftx]], [[Resolution|resolution]] 4.50&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[6ftx]] is a 13 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6FTX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6FTX FirstGlance]. <br>
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<table><tr><td colspan='2'>[[6ftx]] is a 13 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens], [https://en.wikipedia.org/wiki/Petromyzon_marinus Petromyzon marinus], [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae], [https://en.wikipedia.org/wiki/Xenopus_laevis Xenopus laevis], [https://en.wikipedia.org/wiki/Xenopus_tropicalis Xenopus tropicalis] 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=6FTX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6FTX FirstGlance]. <br>
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</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></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 4.5&#8491;</td></tr>
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<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=6ftx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ftx OCA], [http://pdbe.org/6ftx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ftx RCSB], [http://www.ebi.ac.uk/pdbsum/6ftx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ftx ProSAT]</span></td></tr>
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<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></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6ftx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ftx OCA], [https://pdbe.org/6ftx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ftx RCSB], [https://www.ebi.ac.uk/pdbsum/6ftx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ftx ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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[[http://www.uniprot.org/uniprot/H2A1_XENLA H2A1_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/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. [[http://www.uniprot.org/uniprot/UBB_HUMAN UBB_HUMAN]] Ubiquitin exists either covalently attached to another protein, or free (unanchored). When covalently bound, it is conjugated to target proteins via an isopeptide bond either as a monomer (monoubiquitin), a polymer linked via different Lys residues of the ubiquitin (polyubiquitin chains) or a linear polymer linked via the initiator Met of the ubiquitin (linear polyubiquitin chains). Polyubiquitin chains, when attached to a target protein, have different functions depending on the Lys residue of the ubiquitin that is linked: Lys-6-linked may be involved in DNA repair; Lys-11-linked is involved in ERAD (endoplasmic reticulum-associated degradation) and in cell-cycle regulation; Lys-29-linked is involved in lysosomal degradation; Lys-33-linked is involved in kinase modification; Lys-48-linked is involved in protein degradation via the proteasome; Lys-63-linked is involved in endocytosis, DNA-damage responses as well as in signaling processes leading to activation of the transcription factor NF-kappa-B. Linear polymer chains formed via attachment by the initiator Met lead to cell signaling. Ubiquitin is usually conjugated to Lys residues of target proteins, however, in rare cases, conjugation to Cys or Ser residues has been observed. When polyubiquitin is free (unanchored-polyubiquitin), it also has distinct roles, such as in activation of protein kinases, and in signaling.<ref>PMID:16543144</ref> <ref>PMID:19754430</ref> [[http://www.uniprot.org/uniprot/H3C_XENLA H3C_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.
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[https://www.uniprot.org/uniprot/S4RAZ3_PETMA S4RAZ3_PETMA]
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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ATP-dependent chromatin remodelling proteins represent a diverse family of proteins that share ATPase domains that are adapted to regulate protein-DNA interactions. Here we present structures of the Saccharomyces cerevisiae Chd1 protein engaged with nucleosomes in the presence of the transition state mimic ADP-beryllium fluoride. The path of DNA strands through the ATPase domains indicates the presence of contacts conserved with single strand translocases and additional contacts with both strands that are unique to Snf2 related proteins. The structure provides connectivity between rearrangement of ATPase lobes to a closed, nucleotide bound state and the sensing of linker DNA. Two turns of linker DNA are prised off the surface of the histone octamer as a result of Chd1 binding, and both the histone H3 tail and ubiquitin conjugated to lysine 120 are re-orientated towards the unravelled DNA. This indicates how changes to nucleosome structure can alter the way in which histone epitopes are presented.
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Structure of the chromatin remodelling enzyme Chd1 bound to a ubiquitinylated nucleosome.,Sundaramoorthy R, Hughes AL, El-Mkami H, Norman DG, Ferreira H, Owen-Hughes T Elife. 2018 Aug 6;7. pii: 35720. doi: 10.7554/eLife.35720. PMID:30079888<ref>PMID:30079888</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 6ftx" style="background-color:#fffaf0;"></div>
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==See Also==
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*[[Chromodomain-helicase-DNA-binding protein 3D structures|Chromodomain-helicase-DNA-binding protein 3D structures]]
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*[[Histone 3D structures|Histone 3D structures]]
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*[[3D structures of ubiquitin|3D structures of ubiquitin]]
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
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</StructureSection>
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</SX>
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[[Category: Hughes, A]]
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[[Category: Homo sapiens]]
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[[Category: Norman, D G]]
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[[Category: Large Structures]]
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[[Category: Owen-hughes, T]]
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[[Category: Petromyzon marinus]]
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[[Category: Sundaramoorthy, R]]
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[[Category: Saccharomyces cerevisiae]]
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[[Category: Chromatin remodeller]]
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[[Category: Synthetic construct]]
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[[Category: Motor protein]]
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[[Category: Xenopus laevis]]
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[[Category: Xenopus tropicalis]]
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[[Category: Hughes A]]
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[[Category: Norman DG]]
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[[Category: Owen-hughes T]]
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[[Category: Sundaramoorthy R]]

Current revision

Structure of the chromatin remodelling enzyme Chd1 bound to a ubiquitinylated nucleosome

6ftx, resolution 4.50Å

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