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	Structures of dynamic interactors at native proteasomes by PhIX-MS and cryo-electron microscopy.
Journal, issue, pages	Mol Cell, Vol. 86, Issue 15, Page 3067-3085.e13, Year 2026
Publish date	Aug 6, 2026
Authors	Kitaik Lee / Hitendra Negi / Xiang Chen / Katerina Atallah-Yunes / Sophia Truslow / Rithik E Castelino / Mary R Guest / Anthony M Ciancone / Xiuxiu Lu / Sergey G Tarasov / Raj Chari / Kylie J Walters / Francis J O'Reilly /
PubMed Abstract	Molecular machines rely on dynamic, low-affinity interactions to perform their functional roles. We developed PhIX-MS (photo-induced in situ crosslinking-mass spectrometry), a structural proteomics ...Molecular machines rely on dynamic, low-affinity interactions to perform their functional roles. We developed PhIX-MS (photo-induced in situ crosslinking-mass spectrometry), a structural proteomics workflow to capture topological information for such transient interactions in cells by UV-activated crosslinking. Applying PhIX-MS with cryo-electron microscopy (cryo-EM) to proteasomes, we mapped the redox sensor TXNL1 at the proteasome regulatory particle (RP), including its dynamic thioredoxin-like domain near RPN2/PSMD1 and RPN13/ADRM1, where it is ideal for reducing substrates prior to proteolysis. RPs without the proteolytic core particle (CP) were structurally resolved while bound to TXNL1 and/or the chaperone PSMD5/S5b, which inserts its C terminus into the ATPase pore, causing extensive structural rearrangements. Additionally, PhIX-MS and AlphaFold identified the ubiquitin ligase UBE3C/Hul5 at RPN2, RPN3, and a dynamic RPN10 region, tethering UBE3C above the substrate entry channel. Our integrative approach enables the localization of native, low-affinity protein interactions and is broadly applicable to dynamic macromolecular assemblies.
External links	Mol Cell / PubMed:42476128
Methods	EM (single particle)
Resolution	3.02 - 5.35 Å
Structure data	71737 9pmj EMDB-71737, PDB-9pmj: Human 19S proteasome bound to TXNL1 PITH domain without C-terminus Method: EM (single particle) / Resolution: 4.22 Å 71740 9pmo EMDB-71740, PDB-9pmo: Human 26S proteasome bound to TXNL1 with opened gate of core particle Method: EM (single particle) / Resolution: 3.82 Å 71741 9pmq EMDB-71741, PDB-9pmq: Human 26S proteasome bound to TXNL1 with closed gate of core particle Method: EM (single particle) / Resolution: 4.0 Å EMDB-71791: Human 19S proteasome regulatory particle (RP) without observing TXNL1 PITH domain bound Method: EM (single particle) / Resolution: 3.92 Å EMDB-71795: Human 19S proteasome regulatory particle (RP) without observing TXNL1 PITH domain bound but with extra density adjacent to RPT1/RPT2 Method: EM (single particle) / Resolution: 4.24 Å 71810 9pro EMDB-71810, PDB-9pro: Human 19S proteasome bound to TXNL1 PITH domain and PSMD5 Method: EM (single particle) / Resolution: 4.07 Å 71813 9prt EMDB-71813, PDB-9prt: Human 19S proteasome bound to TXNL1 PITH domain but with low density for RPT1, RPT2, and RPN1 Method: EM (single particle) / Resolution: 3.02 Å 76283 12bm EMDB-76283, PDB-12bm: Human 19S proteasome bound to TXNL1 PITH domain state 2 Method: EM (single particle) / Resolution: 3.89 Å EMDB-76415: Human 19S proteasome regulatory particle bound to TXNL1 PITH domain and p28 Method: EM (single particle) / Resolution: 5.35 Å
Chemicals	ChemComp-ADP: ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying moleculeYM ChemComp-AGS: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogueYM ChemComp-MG: Unknown entry ChemComp-ZN: Unknown entry
Source	homo sapiens (human)
Keywords	HYDROLASE / Proteasome / 19S / RP / TXNL1 / 26S / PSMD5