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	Cryo-EM structural analyses reveal plant-specific adaptations of the CDC48 unfoldase.
Journal, issue, pages	Plant Commun, Vol. 7, Issue 1, Page 101572, Year 2026
Publish date	Jan 12, 2026
Authors	Brandon Huntington / Anandsukeerthi Sandholu / Jun Wang / Junrui Zhang / Lingyun Zhao / Bilal M Qureshi / Umar F Shahul Hameed / Stefan T Arold /
PubMed Abstract	Targeted protein degradation through the CDC48 unfoldase enables the maintenance and rapid adaptation of proteomes across eukaryotes. However, the substantial differences among animals, fungi, and ...Targeted protein degradation through the CDC48 unfoldase enables the maintenance and rapid adaptation of proteomes across eukaryotes. However, the substantial differences among animals, fungi, and plants presumably drove extensive adaptation of CDC48-mediated degradation. Although animal and fungal CDC48 systems have shown structural and functional preservation, comparable analysis has been lacking for plants. We determined the structural and functional characteristics of Arabidopsis thaliana CDC48A in multiple states and in complex with the target-identifying cofactors UFD1 and NPL4. Our analysis revealed several features that distinguish AtCDC48A from its animal and yeast counterparts despite 80% sequence identity. Key findings include that AtCDC48A exhibits distinct domain dynamics and engages AtNPL4 in a unique manner. Moreover, AtNPL4 and AtUFD1 do not form an obligate heterodimer; instead, AtNPL4 can independently bind to AtCDC48A and mediate target degradation, although their combined action is synergistic. An evolutionary analysis indicates that these Arabidopsis features are conserved across plants and represent the ancestral state of eukaryotic CDC48 systems. Collectively, our findings suggest that plant CDC48 retains a more modular and combinatorial mode of cofactor usage, highlighting a specific adaptation of targeted protein degradation in plants.
External links	Plant Commun / PubMed:41137397
Methods	EM (single particle) / X-ray diffraction
Resolution	2.6 - 3.9 Å
Structure data	63608 9m3v EMDB-63608, PDB-9m3v: Arabidopsis thaliana CDC48A, nucleotide-free (Apo) Method: EM (single particle) / Resolution: 3.9 Å 63609 9m3w EMDB-63609, PDB-9m3w: Arabidopsis thaliana CDC48A bound to AMP-PNP (AMPPNP-Up) Method: EM (single particle) / Resolution: 3.2 Å 63610 9m3x EMDB-63610, PDB-9m3x: Arabidopsis thaliana CDC48A bound to AMP-PNP (AMPPNP-Down) Method: EM (single particle) / Resolution: 3.3 Å 63611 9m3y EMDB-63611, PDB-9m3y: Arabidopsis thaliana CDC48A bound to ADP Method: EM (single particle) / Resolution: 3.0 Å 63612 9m3z EMDB-63612, PDB-9m3z: Arabidopsis thaliana CDC48A-NPL4-UFD1B (AtCNU) complex Method: EM (single particle) / Resolution: 3.9 Å PDB-9m4g: Structure of AtCDC48 N-domain Method: X-RAY DIFFRACTION / Resolution: 2.6 Å PDB-9m4n: Structure of AtCDC48 Method: X-RAY DIFFRACTION / Resolution: 3.45 Å
Chemicals	ChemComp-ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogueYM ChemComp-MG: Unknown entry ChemComp-ADP: ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying moleculeYM ChemComp-PO4: PHOSPHATE ION ChemComp-HOH: WATER
Source	arabidopsis thaliana (thale cress)
Keywords	PLANT PROTEIN / Targeted protein degradation / plant protein quality control / AAA+ ATPase / cryo-EM / adaptation / ubiquitin-proteasome system / p97/VCP/CDC48 / Ubiquitin-proteasome / Unfoldase / AAA ATPase / Hexamer / ATP-dependent chaperone / Protein unfollding