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 and mechanistic insights into the DNA glycosylase AAG-mediated base excision in nucleosome.
Journal, issue, pages	Cell Discov, Vol. 9, Issue 1, Page 62, Year 2023
Publish date	Jun 20, 2023
Authors	Lvqin Zheng / Bin Tsai / Ning Gao /
PubMed Abstract	The engagement of a DNA glycosylase with a damaged DNA base marks the initiation of base excision repair. Nucleosome-based packaging of eukaryotic genome obstructs DNA accessibility, and how DNA ...The engagement of a DNA glycosylase with a damaged DNA base marks the initiation of base excision repair. Nucleosome-based packaging of eukaryotic genome obstructs DNA accessibility, and how DNA glycosylases locate the substrate site on nucleosomes is currently unclear. Here, we report cryo-electron microscopy structures of nucleosomes bearing a deoxyinosine (DI) in various geometric positions and structures of them in complex with the DNA glycosylase AAG. The apo nucleosome structures show that the presence of a DI alone perturbs nucleosomal DNA globally, leading to a general weakening of the interface between DNA and the histone core and greater flexibility for the exit/entry of the nucleosomal DNA. AAG makes use of this nucleosomal plasticity and imposes further local deformation of the DNA through formation of the stable enzyme-substrate complex. Mechanistically, local distortion augmentation, translation/rotational register shift and partial opening of the nucleosome are employed by AAG to cope with substrate sites in fully exposed, occluded and completely buried positions, respectively. Our findings reveal the molecular basis for the DI-induced modification on the structural dynamics of the nucleosome and elucidate how the DNA glycosylase AAG accesses damaged sites on the nucleosome with different solution accessibility.
External links	Cell Discov / PubMed:37339965 / PubMed Central
Methods	EM (single particle)
Resolution	2.8 - 3.1 Å
Structure data	33171 7xfc EMDB-33171, PDB-7xfc: Structure of nucleosome-DI complex (-30I, Apo state) Method: EM (single particle) / Resolution: 2.9 Å 33172 7xfh EMDB-33172, PDB-7xfh: Structure of nucleosome-AAG complex (A-30I, post-catalytic state) Method: EM (single particle) / Resolution: 2.9 Å 33173 7xfi EMDB-33173, PDB-7xfi: Structure of nucleosome-DI complex (-50I, Apo state) Method: EM (single particle) / Resolution: 2.9 Å 33174 7xfj EMDB-33174, PDB-7xfj: Structure of nucleosome-AAG complex (T-50I, post-catalytic state) Method: EM (single particle) / Resolution: 3.0 Å 33175 7xfl EMDB-33175, PDB-7xfl: Structure of nucleosome-AAG complex (A-53I, free state) Method: EM (single particle) / Resolution: 2.8 Å 33176 7xfm EMDB-33176, PDB-7xfm: Structure of nucleosome-AAG complex (A-53I, post-catalytic state) Method: EM (single particle) / Resolution: 3.1 Å 33177 7xfn EMDB-33177, PDB-7xfn: Structure of nucleosome-DI complex (-55I, Apo state) Method: EM (single particle) / Resolution: 2.8 Å 33322 7xnp EMDB-33322, PDB-7xnp: Structure of nucleosome-AAG complex (A-55I, post-catalytic state) Method: EM (single particle) / Resolution: 2.9 Å
Source	xenopus laevis (African clawed frog) homo sapiens (human)
Keywords	DNA BINDING PROTEIN/DNA / Nucleosome / AAG / DNA repair / Base excision repair / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex / Cryo-EM / Cyro-EM