6CDD
Npl4 zinc finger and MPN domains (Chaetomium thermophilum)
Summary for 6CDD
| Entry DOI | 10.2210/pdb6cdd/pdb |
| Descriptor | Npl4 zinc finger, ZINC ION (3 entities in total) |
| Functional Keywords | aaa atpase cofactor, zinc finger, mpn, protein binding |
| Biological source | Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) |
| Total number of polymer chains | 2 |
| Total formula weight | 107493.08 |
| Authors | Bodnar, N.O.,Rapoport, T.A. (deposition date: 2018-02-08, release date: 2018-07-04, Last modification date: 2024-04-03) |
| Primary citation | Bodnar, N.O.,Kim, K.H.,Ji, Z.,Wales, T.E.,Svetlov, V.,Nudler, E.,Engen, J.R.,Walz, T.,Rapoport, T.A. Structure of the Cdc48 ATPase with its ubiquitin-binding cofactor Ufd1-Npl4. Nat. Struct. Mol. Biol., 25:616-622, 2018 Cited by PubMed Abstract: 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-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. PubMed: 29967539DOI: 10.1038/s41594-018-0085-x PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.58233712092 Å) |
Structure validation
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