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	Structure of an activated DNA-PK and its implications for NHEJ.
Journal, issue, pages	Mol Cell, Vol. 81, Issue 4, Page 801-810.e3, Year 2021
Publish date	Feb 18, 2021
Authors	Xuemin Chen / Xiang Xu / Yun Chen / Joyce C Cheung / Huaibin Wang / Jiansen Jiang / Natalia de Val / Tara Fox / Martin Gellert / Wei Yang /
PubMed Abstract	DNA-dependent protein kinase (DNA-PK), like all phosphatidylinositol 3-kinase-related kinases (PIKKs), is composed of conserved FAT and kinase domains (FATKINs) along with solenoid structures made of ...DNA-dependent protein kinase (DNA-PK), like all phosphatidylinositol 3-kinase-related kinases (PIKKs), is composed of conserved FAT and kinase domains (FATKINs) along with solenoid structures made of HEAT repeats. These kinases are activated in response to cellular stress signals, but the mechanisms governing activation and regulation remain unresolved. For DNA-PK, all existing structures represent inactive states with resolution limited to 4.3 Å at best. Here, we report the cryoelectron microscopy (cryo-EM) structures of DNA-PKcs (DNA-PK catalytic subunit) bound to a DNA end or complexed with Ku70/80 and DNA in both inactive and activated forms at resolutions of 3.7 Å overall and 3.2 Å for FATKINs. These structures reveal the sequential transition of DNA-PK from inactive to activated forms. Most notably, activation of the kinase involves previously unknown stretching and twisting within individual solenoid segments and loosens DNA-end binding. This unprecedented structural plasticity of helical repeats may be a general regulatory mechanism of HEAT-repeat proteins.
External links	Mol Cell / PubMed:33385326 / PubMed Central
Methods	EM (single particle) / X-ray diffraction
Resolution	3.21 - 4.3 Å
Structure data	22618 7k0y EMDB-22618, PDB-7k0y: Cryo-EM structure of activated-form DNA-PK (complex VI) Method: EM (single particle) / Resolution: 3.7 Å 22619 7k10 EMDB-22619, PDB-7k10: CryoEM structure of activated-form FATKIN domain of DNA-PK Method: EM (single particle) / Resolution: 3.3 Å 22620 7k11 EMDB-22620, PDB-7k11: CryoEM structure of inactivated-form FATKIN domain of DNA-PK Method: EM (single particle) / Resolution: 3.21 Å 22622 7k19 EMDB-22622, PDB-7k19: CryoEM structure of DNA-PK catalytic subunit complexed with DNA (Complex I) Method: EM (single particle) / Resolution: 4.3 Å 22623 7k1b EMDB-22623, PDB-7k1b: CryoEM structure of DNA-PK catalytic subunit complexed with DNA (Complex II) Method: EM (single particle) / Resolution: 4.3 Å 22624 7k1j EMDB-22624, PDB-7k1j: CryoEM structure of inactivated-form DNA-PK (Complex III) Method: EM (single particle) / Resolution: 3.9 Å 22625 7k1k EMDB-22625, PDB-7k1k: CryoEM structure of inactivated-form DNA-PK (Complex IV) Method: EM (single particle) / Resolution: 4.1 Å 22626 7k1n EMDB-22626, PDB-7k1n: CryoEM structure of inactivated-form DNA-PK (Complex V) Method: EM (single particle) / Resolution: 3.9 Å PDB-7k17: Re-refined crystal structure of DNA-dependent protein kinase catalytic subunit complexed with Ku80 C-terminal helix Method: X-RAY DIFFRACTION / Resolution: 4.3 Å
Source	homo sapiens (human) synthetic construct (others)
Keywords	DNA BINDING PROTEIN/DNA / DNA-dependent Protein Kinase / DNA repair / NHEJ / V(D)J recombination / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex / PIKK kinase