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      The structure of human CST reveals a decameric assembly bound to telomeric DNA

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          Abstract

          The CTC1-STN1-TEN1 (CST) complex is essential for telomere maintenance and resolution of stalled replication forks genome-wide. Here, we report the 3.0-angstrom cryo–electron microscopy structure of human CST bound to telomeric single-stranded DNA (ssDNA), which assembles as a decameric supercomplex. The atomic model of the 134-kilodalton CTC1 subunit, built almost entirely de novo, reveals the overall architecture of CST and the DNA-binding anchor site. The carboxyl-terminal domain of STN1 interacts with CTC1 at two separate docking sites, allowing allosteric mediation of CST decamer assembly. Furthermore, ssDNA appears to staple two monomers to nucleate decamer assembly. CTC1 has stronger structural similarity to Replication Protein A than the expected similarity to yeast Cdc13. The decameric structure suggests that CST can organize ssDNA analogously to the nucleosome’s organization of double-stranded DNA.

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          Sampling the conformational space of the catalytic subunit of human γ-secretase

          Xiao-chen Bai, Eeson Rajendra, Guanghui Yang … (2015)
          Human γ-secretase is an intra-membrane protease that cleaves many different substrates. Aberrant cleavage of Notch is implicated in cancer, while abnormalities in cutting amyloid precursor protein lead to Alzheimer's disease. Our previous cryo-EM structure of γ-secretase revealed considerable disorder in its catalytic subunit presenilin. Here, we describe an image classification procedure that characterizes molecular plasticity at the secondary structure level, and apply this method to identify three distinct conformations in our previous sample. In one of these conformations, an additional transmembrane helix is visible that cannot be attributed to the known components of γ-secretase. In addition, we present a γ-secretase structure in complex with the dipeptidic inhibitor N-[N-(3,5-difluorophenacetyl)-L-alanyl]-S-phenylglycine t-butyl ester (DAPT). Our results reveal how conformational mobility in the second and sixth transmembrane helices of presenilin is greatly reduced upon binding of DAPT or the additional helix, and form the basis for a new model of how substrate enters the transmembrane domain. DOI: http://dx.doi.org/10.7554/eLife.11182.001
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            Benchmarking fold detection by DaliLite v.5

            Liisa Holm, Arne Elofsson (2019)
            Protein structure comparison plays a fundamental role in understanding the evolutionary relationships between proteins. Here, we release a new version of the DaliLite standalone software. The novelties are hierarchical search of the structure database organized into sequence based clusters, and remote access to our knowledge base of structural neighbors. The detection of fold, superfamily and family level similarities by DaliLite and state-of-the-art competitors was benchmarked against a manually curated structural classification. Database search strategies were evaluated using Fmax with query-specific thresholds. DaliLite and DeepAlign outperformed TM-score based methods at all levels of the benchmark, and DaliLite outperformed DeepAlign at fold level. Hierarchical and knowledge-based searches got close to the performance of systematic pairwise comparison. The knowledge-based search was four times as efficient as the hierarchical search. The knowledge-based search dynamically adjusts the depth of the search, enabling a trade-off between speed and recall. http://ekhidna2.biocenter.helsinki.fi/dali/README.v5.html. Supplementary data are available at Bioinformatics online.
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              Structure of human POT1 bound to telomeric single-stranded DNA provides a model for chromosome end-protection.

              Ming Lei, Thomas Cech, Elaine Podell (2004)
              The POT1 (protection of telomeres 1) protein binds the single-stranded overhang at the ends of chromosomes in diverse eukaryotes. It is essential for chromosome end-protection in the fission yeast Schizosaccharomyces pombe, and it is involved in regulation of telomere length in human cells. Here, we report the crystal structure at a resolution of 1.73 A of the N-terminal half of human POT1 (hPOT1) protein bound to a telomeric single-stranded DNA (ssDNA) decamer, TTAGGGTTAG, the minimum tight-binding sequence indicated by in vitro binding assays. The structure reveals that hPOT1 contains two oligonucleotide/ oligosaccharide-binding (OB) folds; the N-terminal OB fold binds the first six nucleotides, resembling the structure of the S. pombe Pot1pN-ssDNA complex, whereas the second OB fold binds and protects the 3' end of the ssDNA. These results provide an atomic-resolution model for chromosome end-capping.
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                Author and article information

                Journal
                Title: Science
                Abbreviated Title: Science
                Publisher: American Association for the Advancement of Science (AAAS)
                ISSN (Print): 0036-8075
                ISSN (Electronic): 1095-9203
                Publication date Created: June 04 2020
                Publication date Created: June 05 2020
                Publication date (Electronic): June 04 2020
                Publication date (Print): June 05 2020
                Volume: 368
                Issue: 6495
                Pages: 1081-1085
                Affiliations
                [1 ]Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80303, USA.
                [2 ]BioFrontiers Institute, University of Colorado Boulder, Boulder, CO 80303, USA.
                [3 ]Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO 80303, USA.
                Article
                DOI: 10.1126/science.aaz9649
                PMC ID: 7559292
                PubMed ID: 32499435
                SO-VID: a4a51c13-56f3-4267-b7a3-bea46e94266e
                Copyright © © 2020
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                http://www.sciencemag.org/about/science-licenses-journal-article-reuse

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