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| | ==Cdc48-Npl4 complex in the presence of ATP-gamma-S== | | ==Cdc48-Npl4 complex in the presence of ATP-gamma-S== |
| - | <StructureSection load='6chs' size='340' side='right' caption='[[6chs]], [[Resolution|resolution]] 4.30Å' scene=''> | + | <SX load='6chs' size='340' side='right' viewer='molstar' caption='[[6chs]], [[Resolution|resolution]] 4.30Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6chs]] is a 7 chain structure with sequence from [http://en.wikipedia.org/wiki/Chatd Chatd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CHS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CHS FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6chs]] is a 7 chain structure with sequence from [https://en.wikipedia.org/wiki/Chaetomium_thermophilum_var._thermophilum_DSM_1495 Chaetomium thermophilum var. thermophilum DSM 1495]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CHS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6CHS FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AGS:PHOSPHOTHIOPHOSPHORIC+ACID-ADENYLATE+ESTER'>AGS</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 4.3Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[6cdd|6cdd]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AGS:PHOSPHOTHIOPHOSPHORIC+ACID-ADENYLATE+ESTER'>AGS</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">CTHT_0009420 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=759272 CHATD]), CTHT_0027280 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=759272 CHATD])</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=6chs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6chs OCA], [https://pdbe.org/6chs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6chs RCSB], [https://www.ebi.ac.uk/pdbsum/6chs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6chs 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=6chs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6chs OCA], [http://pdbe.org/6chs PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6chs RCSB], [http://www.ebi.ac.uk/pdbsum/6chs PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6chs ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| - | <div style="background-color:#fffaf0;">
| + | == Function == |
| - | == Publication Abstract from PubMed == | + | [https://www.uniprot.org/uniprot/G0S0B4_CHATD G0S0B4_CHATD] |
| - | Many polyubiquitinated proteins are extracted from membranes or complexes by the conserved ATPase Cdc48 (in yeast; p97 or VCP in mammals) before proteasomal degradation. Each Cdc48 hexamer contains two stacked ATPase rings (D1 and D2) and six N-terminal (N) domains. Cdc48 binds various cofactors, including the Ufd1-Npl4 heterodimer. Here, we report structures of the Cdc48-Ufd1-Npl4 complex from Chaetomium thermophilum. Npl4 interacts through its UBX-like domain with a Cdc48 N domain, and it uses two Zn(2+)-finger domains to anchor the enzymatically inactive Mpr1-Pad1 N-terminal (MPN) domain, homologous to domains found in several isopeptidases, to the top of the D1 ATPase ring. The MPN domain of Npl4 is located above Cdc48's central pore, a position similar to the MPN domain from deubiquitinase Rpn11 in the proteasome. Our results indicate that Npl4 is unique among Cdc48 cofactors and suggest a mechanism for binding and translocation of polyubiquitinated substrates into the ATPase.
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| - | Structure of the Cdc48 ATPase with its ubiquitin-binding cofactor Ufd1-Npl4.,Bodnar NO, Kim KH, Ji Z, Wales TE, Svetlov V, Nudler E, Engen JR, Walz T, Rapoport TA Nat Struct Mol Biol. 2018 Jul;25(7):616-622. doi: 10.1038/s41594-018-0085-x. Epub, 2018 Jul 2. PMID:29967539<ref>PMID:29967539</ref>
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| - | </div>
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| - | <div class="pdbe-citations 6chs" style="background-color:#fffaf0;"></div>
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| - | == References ==
| + | |
| - | <references/>
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| | __TOC__ | | __TOC__ |
| - | </StructureSection> | + | </SX> |
| - | [[Category: Chatd]] | + | [[Category: Chaetomium thermophilum var. thermophilum DSM 1495]] |
| - | [[Category: Bodnar, N O]] | + | [[Category: Large Structures]] |
| - | [[Category: Kim, K H]] | + | [[Category: Bodnar NO]] |
| - | [[Category: Rapoport, T A]] | + | [[Category: Kim KH]] |
| - | [[Category: Walz, T]] | + | [[Category: Rapoport TA]] |
| - | [[Category: Aaa+]] | + | [[Category: Walz T]] |
| - | [[Category: Erad]]
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| - | [[Category: Motor protein]]
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| - | [[Category: Ubiquitin-binding protein]]
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| - | [[Category: Zinc finger]]
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