Editorial: Technical Advances in Cryo-Electron Microscopy

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Evidence for a remodelling of DNA-PK upon autophosphorylation from electron microscopy studies

The multi-subunit DNA-dependent protein kinase (DNA-PK), a crucial player in DNA repair by non-homologous end-joining in higher eukaryotes, consists of a catalytic subunit (DNA-PKcs) and the Ku heterodimer. Ku recruits DNA-PKcs to double-strand breaks, where DNA-PK assembles prior to DNA repair. The interaction of DNA-PK with DNA is regulated via autophosphorylation. Recent SAXS data addressed the conformational changes occurring in the purified catalytic subunit upon autophosphorylation. Here, we present the first structural analysis of the effects of autophosphorylation on the trimeric DNA-PK enzyme, performed by electron microscopy and single particle analysis. We observe a considerable degree of heterogeneity in the autophosphorylated material, which we resolved into subpopulations of intact complex, and separate DNA-PKcs and Ku, by using multivariate statistical analysis and multi-reference alignment on a partitioned particle image data set. The proportion of dimeric oligomers was reduced compared to non-phosphorylated complex, and those dimers remaining showed a substantial variation in mutual monomer orientation. Together, our data indicate a substantial remodelling of DNA-PK holo-enzyme upon autophosphorylation, which is crucial to the release of protein factors from a repaired DNA double-strand break

Structural basis for the inactivation of cytosolic DNA sensing by the vaccinia virus

Detection of cytosolic DNA is a central element of the innate immunity system against viral infection. The Ku heterodimer, a component of the NHEJ pathway of DNA repair in the nucleus, functions as DNA sensor that detects dsDNA of viruses that replicate in the cytoplasm. Vaccinia virus expresses two proteins, C4 and C16, that inactivate DNA sensing and enhance virulence. The structural basis for this is unknown. Here we determine the structure of the C16 – Ku complex using cryoEM. Ku binds dsDNA by a preformed ring but C16 sterically blocks this access route, abrogating binding to a dsDNA end and its insertion into DNA-PK, thereby averting signalling into the downstream innate immunity system. C4 replicates these activities using a domain with 54% identity to C16. Our results reveal how vaccinia virus subverts the capacity of Ku to recognize viral DNA

The structure of the R2TP complex defines a platform for recruiting diverse client proteins to the HSP90 molecular chaperone system

The R2TP complex, comprising the Rvb1p-Rvb2p AAA-ATPases, Tah1p, and Pih1p in yeast, is a special- ized Hsp90 co-chaperone required for the assembly and maturation of multi-subunit complexes. These include the small nucleolar ribonucleoproteins, RNA polymerase II, and complexes containing phosphati- dylinositol-3-kinase-like kinases. The structure and stoichiometry of yeast R2TP and how it couples to Hsp90 are currently unknown. Here, we determine the 3D organization of yeast R2TP using sedimenta- tion velocity analysis and cryo-electron microscopy. The 359-kDa complex comprises one Rvb1p/Rvb2p hetero-hexamer with domains II (DIIs) forming an open basket that accommodates a single copy of Tah1p-Pih1p. Tah1p-Pih1p binding to multiple DII do- mains regulates Rvb1p/Rvb2p ATPase activity. Using domain dissection and cross-linking mass spectro- metry, we identified a unique region of Pih1p that is essential for interaction with Rvb1p/Rvb2p. These data provide a structural basis for understanding how R2TP couples an Hsp90 dimer to a diverse set of client proteins and complexes

Desarrollo de herramientas para el aprendizaje interactivo y experimental del Electromagnetismo en el aula

Depto. de Física de MaterialesFac. de Ciencias FísicasFALSEsubmitte

Structural model of full-length human Ku70–Ku80 heterodimer and its recognition of DNA and DNA-PKcs

Recognition of DNA double-strand breaks during non-homologous end joining is carried out by the Ku70–Ku80 protein, a 150 kDa heterodimer that recruits the DNA repair kinase DNA-dependent protein kinase catalytic subunit (DNA-PKcs) to the lesion. The atomic structure of a truncated Ku70–Ku80 was determined; however, the subunit-specific carboxy-terminal domain of Ku80—essential for binding to DNA-PKcs—was determined only in isolation, and the C-terminal domain of Ku70 was not resolved in its DNA-bound conformation. Both regions are conserved and mediate protein–protein interactions specific to mammals. Here, we reconstruct the three-dimensional structure of the human full-length Ku70–Ku80 dimer at 25 Å resolution, alone and in complex with DNA, by using single-particle electron microscopy. We map the C-terminal regions of both subunits, and their conformational changes after DNA and DNA-PKcs binding to define a molecular model of the functions of these domains during DNA repair in the context of full-length Ku70–Ku80 protein

Three-dimensional structure and regulation of the DNA-dependent protein kinase catalytic subunit (DNA-PKcs)

DNA-PKcs is a large PI3-kinase-related protein kinase (PIKK) that plays a central role in DNA double-strand break (DSB) repair via nonhomologous end joining. Using cryo-electron microscopy we have now generated a ∼13 Å three-dimensional map of DNA-PKcs, revealing the overall architecture and topology of the 4128 residue polypeptide chain and allowing location of domains. The highly conserved C-terminal PIKK catalytic domain forms a central structure from which FAT and FATC domains protrude. Conformational changes observed in these domains on DNA binding suggest that they transduce DNA-induced conformational changes to the catalytic core and regulate kinase activity. The N-terminal segments form long curved tubular-shaped domains based on helical repeats to create interacting surfaces required for macromolecular assembly. Comparison of DNA-PKcs with another PIKK DNA repair factor, ATM, defines a common architecture for this important protein family

XANES and EXAFS study of the local order in nanocrystalline yttria-stabilized zirconia

Under the terms of the Creative Commons Attribution License 3.0 (CC-BY).The local order around Zr and Y atoms of nanocrystalline yttria-stabilized zirconia (YSZ) powders with different grain sizes has been investigated by x-ray absorption spectroscopies. The samples were prepared by means of mechanical alloying with or without subsequent sintering treatment and also by milling commercial YSZ. Our study is motivated by the interest in the electrical properties of grain boundaries and the controversy about the level of disorder in the intergrain regions in nanocrystalline YSZ. The x-ray absorption near edge structure (XANES) analysis indicates that the local order of all the sintered samples is independent of the grain size. This is confirmed by the analysis of the extended x-ray absorption fine structure, which points out also that, in contrast to that found in sintered samples, the local order around the cation in the samples milled without further sintering treatment extends only to the first coordination shell. Finally, the results of ab initio Zr K-edge XANES calculations lead us to conclude that the observed changes of the shape of the white line are not related to a phase transformation but reflects the short-range order present in the as-milled samples. © 2013 American Physical Society.This work was partially supported by Spanish and MAT2011-27573-C04-04 grants, by Junta de Comunidades de Castilla-La Mancha through Project No. PCI-08-0091 and by the Aragón DGA NETOSHIMA grant.Peer Reviewe