Angel Rivera-Calzada

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.

Structural model for the mannose receptor family uncovered by electron microscopy of Endo180 and the mannose receptor

The mannose receptor family comprises four members in mammals, Endo180 (CD280), DEC-205 (CD205), phospholipase A2 receptor (PLA2R) and the mannose receptor (MR, CD206), whose extracellular portion contains a similar domain arrangement: an N-terminal cysteine-rich domain (CysR) followed by a single fibronectin type II domain (FNII) and 8–10 C-type lectin-like domains (CTLDs). These proteins mediate diverse functions ranging from extracellular matrix turnover through collagen uptake to homeostasis and immunity based on sugar recognition. Endo180 and the MR are multivalent transmembrane receptors capable of interacting with multiple ligands; in both receptors FNII recognizes collagens, and a single CTLD retains lectin activity (CTLD2 in Endo180 and CTLD4 in MR). It is expected that the overall conformation of these multivalent molecules would deeply influence their function as the availability of their binding sites could be altered under different conditions. However, conflicting reports have been published on the three-dimensional arrangement of these receptors. Here, we have used single particle electron microscopy to elucidate the three-dimensional organization of the MR and Endo180. Strikingly, we have found that both receptors display distinct three-dimensional structures, which are, however, conceptually very similar: a bent and compact conformation built upon interactions of the CysR domain and the lone functional CTLD. Biochemical and electron microscopy experiments indicate that, under a low pH mimicking the endosomal environment, both MR and Endo180 experience large conformational changes. We propose a structural model for the mannose receptor family where at least two conformations exist that may serve to regulate differences in ligand selectivity.

Three-dimensional interplay among the ligand- binding domains of the urokinase-plasminogen- activator-receptor-associated protein, Endo180

Endo180, also known as the urokinase plasminogen activator receptor (uPAR)‐associated protein (uPARAP), is one of the four members of the mannose receptor family, and is implicated in extracellular‐matrix remodelling through its interactions with collagens, sugars and uPAR. The extracellular portion of Endo180 contains an amino‐terminal cysteine‐rich domain, a single fibronectin type II domain and eight C‐type lectin‐like domains. We have purified a soluble version of Endo180 and analysed it by single‐particle electron microscopy to obtain a three‐dimensional structure of the N‐terminal part of the protein at a resolution of 17 Å and reveal, for the first time, the interactions between non‐adjacent domains in the mannose receptor family. We show that for Endo180, the cysteine‐rich domain contacts the second C‐type lectin‐like domain, thus providing structural insight into how modulation of its several ligand interactions may regulate Endo180 receptor function.

Electron microscopy of Xrcc4 and the DNA ligase IV-Xrcc4 DNA repair complex.

The DNA ligase IV-Xrcc4 complex is responsible for the ligation of broken DNA ends in the non-homologous end-joining (NHEJ) pathway of DNA double strand break repair in mammals. Mutations in DNA ligase IV (Lig4) lead to immunodeficiency and radiosensitivity in humans. Only partial structural information for Lig4 and Xrcc4 is available, while the structure of the full-length proteins and their arrangement within the Lig4-Xrcc4 complex is unknown. The C-terminal domain of Xrcc4, whose structure has not been solved, contains phosphorylation sites for DNA-PKcs and is phylogenetically conserved, indicative of a regulatory role in NHEJ. Here, we have purified full length Xrcc4 and the Lig4-Xrcc4 complex, and analysed their structure by single-particle electron microscopy. The three-dimensional structure of Xrcc4 at a resolution of approximately 37A reveals that the C-terminus of Xrcc4 forms a dimeric globular domain connected to the N-terminus by a coiled-coil. The N- and C-terminal domains of Xrcc4 locate at opposite ends of an elongated molecule. The electron microscopy images of the Lig4-Xrcc4 complex were examined by two-dimensional image processing and a double-labelling strategy, identifying the site of the C-terminus of Xrcc4 and the catalytic core of Lig4 within the complex. The catalytic domains of Lig4 were found to be in the vicinity of the N-terminus of Xrcc4. We provide a first sight of the structural organization of the Lig4-Xrcc4 complex, which suggests that the BRCT domains could provide the link of the ligase to Xrcc4 while permitting some movements of the catalytic domains of Lig4. This arrangement may facilitate the ligation of diverse configurations of damaged DNA.

A new protein carrying an NmrA-like domain is required for cell differentiation and development in Dictyostelium discoideum

We have isolated a Dictyostelium mutant unable to induce expression of the prestalk-specific marker ecmB in monolayer assays. The disrupted gene, padA, leads to a range of phenotypic defects in growth and development. We show that padA is essential for growth, and we have generated a thermosensitive mutant allele, padA(-). At the permissive temperature, mutant cells grow poorly; they remain longer at the slug stage during development and are defective in terminal differentiation. At the restrictive temperature, growth is completely blocked, while development is permanently arrested prior to culmination. padA(-) slugs are deficient in prestalk A cell differentiation and present an abnormal ecmB expression pattern. Sequence comparisons and predicted three-dimensional structure analyses show that PadA carries an NmrA-like domain. NmrA is a negative transcriptional regulator involved in nitrogen metabolite repression in Aspergillus nidulans. PadA predicted structure shows a NAD(P)(+)-binding domain, which we demonstrate that is essential for function. We show that padA(-) development is more sensitive to ammonia than wild-type cells and two ammonium transporters, amtA and amtC, appear derepressed during padA(-) development. Our data suggest that PadA belongs to a new family of NAD(P)(+)-binding proteins that link metabolic changes to gene expression and is required for growth and normal development.

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.

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

Summary The R2TP complex, comprising the Rvb1p-Rvb2p AAA-ATPases, Tah1p, and Pih1p in yeast, is a specialized 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 phosphatidylinositol-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 sedimentation 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 domains regulates Rvb1p/Rvb2p ATPase activity. Using domain dissection and cross-linking mass spectrometry, 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.

3D Structure of DNA Repair Macromolecular Complexes Participating in Non-Homologous End-Joining (NHEJ)

Double-strand DNA breaks (DSBs) fracture the chromosomes, generating genomic instability and chromosomal translocations which favor tumor transformation [1]. Cells use two mechanisms to repair these DSBs, Homologous Recombination (HR) and Non-Homologous End-Joining (NHEJ) [2]. NHEJ is the most frequent DNA repair pathway in mammalian cells but this is restricted to G0 and G1 phases of the cell cycle. During NHEJ the broken ends are processed with potential loss of genetic information, and the backbones ligated without using a template. In addition, the NHEJ system repairs programmed DSBs generated as intermediates during V(D)J recombination in lymphocytes. Several recessive human syndromes and diseases can be related to mutations of proteins that participate in these DNA repair pathways.