5xit

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'''Unreleased structure'''
 
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The entry 5xit is ON HOLD until Paper Publication
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==Crystal structure of RNF168 UDM1 in complex with Lys63-linked diubiquitin, form II==
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<StructureSection load='5xit' size='340' side='right'caption='[[5xit]], [[Resolution|resolution]] 2.25&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[5xit]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XIT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XIT FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.25&#8491;</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=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=PR:PRASEODYMIUM+ION'>PR</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=5xit FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xit OCA], [https://pdbe.org/5xit PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xit RCSB], [https://www.ebi.ac.uk/pdbsum/5xit PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xit ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/RS27A_MOUSE RS27A_MOUSE] 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:19754430</ref> 40S Ribosomal protein S27a: Component of the 40S subunit of the ribosome.<ref>PMID:19754430</ref>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The E3 ubiquitin (Ub) ligase RNF168 plays a critical role in the initiation of the DNA damage response to double-strand breaks (DSBs). The recruitment of RNF168 by ubiquitylated targets involves two distinct regions, Ub-dependent DSB recruitment module (UDM) 1 and UDM2. Here we report the crystal structures of the complex between UDM1 and Lys63-linked diUb (K63-Ub2) and that between the C-terminally truncated UDM2 (UDM2DeltaC) and K63-Ub2. In both structures, UDM1 and UDM2DeltaC fold as a single alpha-helix. Their simultaneous bindings to the distal and proximal Ub moieties provide specificity for Lys63-linked Ub chains. Structural and biochemical analyses of UDM1 elucidate an Ub-binding mechanism between UDM1 and polyubiquitylated targets. Mutations of Ub-interacting residues in UDM2 prevent the accumulation of RNF168 to DSB sites in U2OS cells, whereas those in UDM1 have little effect, suggesting that the interaction of UDM2 with ubiquitylated and polyubiquitylated targets mainly contributes to the RNF168 recruitment.
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Authors: Takahashi, T.S., Sato, Y., Fukai, S.
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Structural insights into two distinct binding modules for Lys63-linked polyubiquitin chains in RNF168.,Takahashi TS, Hirade Y, Toma A, Sato Y, Yamagata A, Goto-Ito S, Tomita A, Nakada S, Fukai S Nat Commun. 2018 Jan 12;9(1):170. doi: 10.1038/s41467-017-02345-y. PMID:29330428<ref>PMID:29330428</ref>
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Description: Crystal structure of the ubiquitin effector
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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[[Category: Unreleased Structures]]
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</div>
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[[Category: Sato, Y]]
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<div class="pdbe-citations 5xit" style="background-color:#fffaf0;"></div>
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[[Category: Takahashi, T.S]]
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== References ==
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[[Category: Fukai, S]]
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Homo sapiens]]
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[[Category: Large Structures]]
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[[Category: Mus musculus]]
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[[Category: Fukai S]]
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[[Category: Sato Y]]
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[[Category: Takahashi TS]]

Current revision

Crystal structure of RNF168 UDM1 in complex with Lys63-linked diubiquitin, form II

PDB ID 5xit

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