Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Structural insights into the ubiquitin-independent midnolin-proteasome pathway.
Journal, issue, pages	Proc Natl Acad Sci U S A, Vol. 122, Issue 19, Page e2505345122, Year 2025
Publish date	May 13, 2025
Authors	Nagesh Peddada / Xue Zhong / Yan Yin / Danielle Renee Lazaro / Jianhui Wang / Stephen Lyon / Jin Huk Choi / Xiao-Chen Bai / Eva Marie Y Moresco / Bruce Beutler /
PubMed Abstract	The protein midnolin (MIDN) augments proteasome activity in lymphocytes and dramatically facilitates the survival and proliferation of B-lymphoid malignancies. MIDN binds both to proteasomes and to ...The protein midnolin (MIDN) augments proteasome activity in lymphocytes and dramatically facilitates the survival and proliferation of B-lymphoid malignancies. MIDN binds both to proteasomes and to substrates, but the mode of interaction with the proteasome is unknown, and the mechanism by which MIDN facilitates substrate degradation in a ubiquitin-independent manner is incompletely understood. Here, we present cryoelectron microscopy (cryo-EM) structures of the substrate-engaged, MIDN-bound human proteasome in two conformational states. MIDN induces proteasome conformations similarly to ubiquitinated substrates by using its ubiquitin-like domain to bind to the deubiquitinase RPN11 (PSMD14). By simultaneously binding to RPN1 (PSMD2) with its C-terminal α-helix, MIDN positions its substrate-carrying Catch domain above the proteasome ATPase channel through which substrates are translocated before degradation. Our findings suggest that both ubiquitin-like domain and C-terminal α-helix must bind to the proteasome for MIDN to stimulate proteasome activity.
External links	Proc Natl Acad Sci U S A / PubMed:40339123
Methods	EM (single particle)
Resolution	2.8 - 3.84 Å
Structure data	EMDB-49497: Consensus map of MIDN-bound 26S proteasome, EB-state Method: EM (single particle) / Resolution: 2.8 Å EMDB-49498: Locally Refined map of RP(19S) in substrate-engaged MIDN-bound 26S Proteasome, EB-MIDN state Method: EM (single particle) / Resolution: 2.8 Å EMDB-49499: Locally refined map of RPN1-MIDN_alphaHelix-C Method: EM (single particle) / Resolution: 2.8 Å EMDB-49500: Locally refined map of RPN11-MIDN_UBL domain Method: EM (single particle) / Resolution: 2.82 Å EMDB-49501: Consensus map of 26S proteasome bound to MIDN, EB-MIDN_UBL state Method: EM (single particle) / Resolution: 3.0 Å EMDB-49502: Locally refined map of RP(19S) of MIDN-bound 26S proteasome in EB-MIDN_UBL state Method: EM (single particle) / Resolution: 3.23 Å EMDB-49503: Consensus map of substrate-free 26S proteasome in presence MG-132 Method: EM (single particle) / Resolution: 2.9 Å EMDB-49504: Focused map of RP (19S) substrate-free MIDN-free 26S proteasome, SA-like state with MG-132 Method: EM (single particle) / Resolution: 2.9 Å EMDB-49505: Consensus map of substrate engaged MIDN-bound 26S proteasome, ED-state Method: EM (single particle) / Resolution: 3.81 Å EMDB-49506: Locally Refined map of RP(19S) in substrate-engaged MIDN-bound 26S Proteasome, ED-MIDN state Method: EM (single particle) / Resolution: 3.84 Å 49507 9nkf EMDB-49507, PDB-9nkf: Structure of human substrate-free 26S proteasome in the presence of ATPgS and MG-132,SA-like state (composite map) Method: EM (single particle) / Resolution: 2.9 Å 49508 9nkg EMDB-49508, PDB-9nkg: Structure of substrate engaged MIDN-bound human 26S proteasome, EB-MIDN (Composite map) Method: EM (single particle) / Resolution: 2.8 Å 49509 9nki EMDB-49509, PDB-9nki: Structure of substrate engaged MIDN-bound human 26S proteasome, EB MIDN_UBL state (Composite map) Method: EM (single particle) / Resolution: 2.94 Å 49510 9nkj EMDB-49510, PDB-9nkj: Structure of substrates-engaged MIDN-bound human 26S proteasome,ED-MIDN state (Composite map) Method: EM (single particle) / Resolution: 3.84 Å
Chemicals	ChemComp-ATP: ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying moleculeYM ChemComp-MG: Unknown entry ChemComp-ADP: ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying moleculeYM ChemComp-LDZ: N-[(benzyloxy)carbonyl]-L-leucyl-N-[(2S)-4-methyl-1-oxopentan-2-yl]-L-leucinamide / inhibitorYM ChemComp-ZN*: Unknown entry
Source	homo sapiens (human)
Keywords	IMMUNE SYSTEM / Apo state / proteasome / Midnolin / substrate-free 26S / MG-132 / Ubiquitin-indepedent / MIDN-bound 26S complex / MIDN-UBL / 26S complex / ED-state