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      Structural characterisation of the Chaetomium thermophilum Chl1 helicase

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          Abstract

          Chl1 is a member of the XPD family of 5’-3’ DNA helicases, which perform a variety of roles in genome maintenance and transmission. They possess a variety of unique structural features, including the presence of a highly variable, partially-ordered insertion in the helicase domain 1. Chl1 has been shown to be required for chromosome segregation in yeast due to its role in the formation of persistent chromosome cohesion during S-phase. Here we present structural and biochemical data to show that Chl1 has the same overall domain organisation as other members of the XPD family, but with some conformational alterations. We also present data suggesting the insert domain in Chl1 regulates its DNA binding.

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          cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination

          A software tool, cryoSPARC, addresses the speed bottleneck in cryo-EM image processing, enabling automated macromolecular structure determination in hours on a desktop computer without requiring a starting model.
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            MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy

            MotionCor2 software corrects for beam-induced sample motion, improving the resolution of cryo-EM reconstructions.
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              New tools for automated high-resolution cryo-EM structure determination in RELION-3

              Here, we describe the third major release of RELION. CPU-based vector acceleration has been added in addition to GPU support, which provides flexibility in use of resources and avoids memory limitations. Reference-free autopicking with Laplacian-of-Gaussian filtering and execution of jobs from python allows non-interactive processing during acquisition, including 2D-classification, de novo model generation and 3D-classification. Per-particle refinement of CTF parameters and correction of estimated beam tilt provides higher resolution reconstructions when particles are at different heights in the ice, and/or coma-free alignment has not been optimal. Ewald sphere curvature correction improves resolution for large particles. We illustrate these developments with publicly available data sets: together with a Bayesian approach to beam-induced motion correction it leads to resolution improvements of 0.2–0.7 Å compared to previous RELION versions.
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                Author and article information

                Contributors
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: Writing – original draftRole: Writing – review & editing
                Role: Methodology
                Role: Investigation
                Role: InvestigationRole: Methodology
                Role: Methodology
                Role: MethodologyRole: Writing – review & editing
                Role: ResourcesRole: SupervisionRole: Writing – review & editing
                Role: ConceptualizationRole: Data curationRole: Funding acquisitionRole: Project administrationRole: SupervisionRole: ValidationRole: Writing – original draftRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS One
                PLoS One
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                10 May 2021
                2021
                : 16
                : 5
                : e0251261
                Affiliations
                [1 ] Structural Biology of Chromosome Segregation Laboratory, The Francis Crick Institute, London, United Kingdom
                [2 ] Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, United Kingdom
                [3 ] Structural Biology Science Technology Platform, The Francis Crick Institute, London, United Kingdom
                [4 ] Proteomics Science Technology Platform, The Francis Crick Institute, London, United Kingdom
                [5 ] Macromolecular Structure Laboratory, The Francis Crick Institute, London, United Kingdom
                [6 ] Chromosome Segregation Laboratory, The Francis Crick Institute, London, United Kingdom
                Tulane University Health Sciences Center, UNITED STATES
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                [¤]

                Current address: Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria

                Author information
                https://orcid.org/0000-0002-2599-0333
                https://orcid.org/0000-0002-3791-2447
                https://orcid.org/0000-0002-6763-3852
                https://orcid.org/0000-0002-3527-6619
                https://orcid.org/0000-0001-5716-7715
                Article
                PONE-D-21-05603
                10.1371/journal.pone.0251261
                8109800
                33970942
                6fc4aa2b-3fa7-4729-89b7-d57a468f62df
                © 2021 Hodáková et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 5 March 2021
                : 22 April 2021
                Page count
                Figures: 7, Tables: 1, Pages: 17
                Funding
                Funded by: funder-id http://dx.doi.org/10.13039/501100000289, Cancer Research UK;
                Award ID: FC001155
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/100004440, Wellcome Trust;
                Award ID: FC001155
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100009187, Medical Research Foundation;
                Award ID: FC001155
                Award Recipient :
                MRS was supported by the Francis Crick Institute, which receives its core funding from Cancer Research UK (FC001155), the Medical Research Council (FC001155) and the Wellcome Trust (FC001155). cancerresearchuk.org wellcome.org ukri.org The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Biology and Life Sciences
                Biochemistry
                Enzymology
                Enzymes
                Helicases
                Biology and Life Sciences
                Biochemistry
                Proteins
                Enzymes
                Helicases
                Biology and life sciences
                Biochemistry
                Proteins
                DNA-binding proteins
                Biology and Life Sciences
                Biochemistry
                Nucleotides
                Research and Analysis Methods
                Specimen Preparation and Treatment
                Staining
                Negative Staining
                Biology and Life Sciences
                Organisms
                Eukaryota
                Fungi
                Yeast
                Physical Sciences
                Chemistry
                Chemical Compounds
                Organic Compounds
                Amino Acids
                Sulfur Containing Amino Acids
                Cysteine
                Physical Sciences
                Chemistry
                Organic Chemistry
                Organic Compounds
                Amino Acids
                Sulfur Containing Amino Acids
                Cysteine
                Biology and Life Sciences
                Biochemistry
                Proteins
                Amino Acids
                Sulfur Containing Amino Acids
                Cysteine
                Research and Analysis Methods
                Separation Processes
                Elution
                Research and Analysis Methods
                Microscopy
                Electron Microscopy
                Electron Cryo-Microscopy
                Custom metadata
                All EM volume files are available from the EMDB database, accession number EMD-12817.

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                Uncategorized

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