4xkl

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'''Unreleased structure'''
 
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The entry 4xkl is ON HOLD until Paper Publication
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==Crystal structure of NDP52 ZF2 in complex with mono-ubiquitin==
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<StructureSection load='4xkl' size='340' side='right'caption='[[4xkl]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[4xkl]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4XKL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4XKL 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]] 2.1&#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=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=4xkl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4xkl OCA], [https://pdbe.org/4xkl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4xkl RCSB], [https://www.ebi.ac.uk/pdbsum/4xkl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4xkl ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/RL40_HUMAN RL40_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> Ribosomal protein L40 is a component of the 60S subunit of the ribosome.<ref>PMID:16543144</ref> <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 autophagy receptor CALCOCO2/NDP52 functions as a bridging adaptor and plays an essential role in the selective autophagic degradation of invading pathogens by specifically recognizing ubiquitin-coated intracellular pathogens and subsequently targeting them to the autophagic machinery; thereby it is required for innate immune defense against a range of infectious pathogens in mammals. However, the mechanistic basis underlying CALCOCO2-mediated specific recognition of ubiqutinated pathogens is still unknown. Here, using biochemical and structural analyses, we demonstrated that the cargo-binding region of CALCOCO2 contains a dynamic unconventional zinc finger as well as a C2H2-type zinc-finger, and only the C2H2-type zinc finger specifically recognizes mono-ubiquitin or poly-ubiquitin chains. In addition to elucidating the specific ubiquitin recognition mechanism of CALCOCO2, the structure of the CALCOCO2 C2H2-type zinc finger in complex with mono-ubiquitin also uncovers a unique zinc finger-binding mode for ubiquitin. Our findings provide mechanistic insight into how CALCOCO2 targets ubiquitin-decorated pathogens for autophagic degradations.
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Authors: Xie, X., Li, F., Wang, Y., Lin, Z., Chen, X., Liu, J., Pan, L.
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Molecular basis of ubiquitin recognition by the autophagy receptor CALCOCO2.,Xie X, Li F, Wang Y, Wang Y, Lin Z, Cheng X, Liu J, Chen C, Pan L Autophagy. 2015;11(10):1775-89. doi: 10.1080/15548627.2015.1082025. PMID:26506893<ref>PMID:26506893</ref>
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Description: Crystal structure of NDP52 ZF2 in complex with mono-ubiquitin
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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: Wang, Y]]
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<div class="pdbe-citations 4xkl" style="background-color:#fffaf0;"></div>
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[[Category: Xie, X]]
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[[Category: Pan, L]]
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==See Also==
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[[Category: Li, F]]
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*[[3D structures of ubiquitin|3D structures of ubiquitin]]
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[[Category: Liu, J]]
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== References ==
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[[Category: Chen, X]]
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<references/>
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[[Category: Lin, Z]]
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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: Chen X]]
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[[Category: Li F]]
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[[Category: Lin Z]]
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[[Category: Liu J]]
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[[Category: Pan L]]
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[[Category: Wang Y]]
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[[Category: Xie X]]

Current revision

Crystal structure of NDP52 ZF2 in complex with mono-ubiquitin

PDB ID 4xkl

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