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      EMRinger: Side-chain-directed model and map validation for 3D Electron Cryomicroscopy

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          Abstract

          Advances in high resolution electron cryomicroscopy (cryo-EM) have been accompanied by the development of validation metrics to independently assess map quality and model geometry. EMRinger assesses the precise fitting of an atomic model into the map during refinement and shows how radiation damage alters scattering from negatively charged amino acids. EMRinger will be useful for monitoring progress in resolving and modeling high-resolution features in cryo-EM.

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          Structure of the TRPV1 ion channel determined by electron cryo-microscopy

          Maofu Liao, Erhu Cao, David Julius … (2013)
          Transient receptor potential (TRP) channels are sensors for a wide range of cellular and environmental signals, but elucidating how these channels respond to physical and chemical stimuli has been hampered by a lack of detailed structural information. Here, we exploit advances in electron cryo-microscopy to determine the structure of a mammalian TRP channel, TRPV1, at 3.4Å resolution, breaking the side-chain resolution barrier for membrane proteins without crystallization. Like voltage-gated channels, TRPV1 exhibits four-fold symmetry around a central ion pathway formed by transmembrane helices S5–S6 and the intervening pore loop, which is flanked by S1–S4 voltage sensor-like domains. TRPV1 has a wide extracellular ‘mouth’ with short selectivity filter. The conserved ‘TRP domain’ interacts with the S4–S5 linker, consistent with its contribution to allosteric modulation. Subunit organization is facilitated by interactions among cytoplasmic domains, including N-terminal ankyrin repeats. These observations provide a structural blueprint for understanding unique aspects of TRP channel function.
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            Rotamer libraries in the 21st century.

            Roland L. Dunbrack (2002)
            Rotamer libraries are widely used in protein structure prediction, protein design, and structure refinement. As the size of the structure data base has increased rapidly in recent years, it has become possible to derive well-refined rotamer libraries using strict criteria for data inclusion and for studying dependence of rotamer populations and dihedral angles on local structural features.
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              The penultimate rotamer library.

              S Lovell, J M Word, J Richardson … (2000)
              All published rotamer libraries contain some rotamers that exhibit impossible internal atomic overlaps if built in ideal geometry with all hydrogen atoms. Removal of uncertain residues (mainly those with B-factors >/=40 or van der Waals overlaps >/=0.4 A) greatly improves the clustering of rotamer populations. Asn, Gln, or His side chains additionally benefit from flipping of their planar terminal groups when required by atomic overlaps or H-bonding. Sensitivity to skew and to the boundaries of chi angle bins is avoided by using modes rather than traditional mean values. Rotamer definitions are listed both as the modal values and in a preferred version that maximizes common atoms between related rotamers. The resulting library shows significant differences from previous ones, differences validated by considering the likelihood of systematic misfitting of models to electron density maps and by plotting changes in rotamer frequency with B-factor. Few rotamers now show atomic overlaps in ideal geometry; those overlaps are relatively small and can be understood in terms of bond angle distortions compensated by favorable interactions. The new library covers 94.5% of examples in the highest quality protein data with 153 rotamers and can make a significant contribution to improving the accuracy of new structures. Proteins 2000;40:389-408. Copyright 2000 Wiley-Liss, Inc.
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                Author and article information

                Journal
                Journal ID (nlm-journal-id): 101215604
                Journal ID (pubmed-jr-id): 32338
                Journal ID (nlm-ta): Nat Methods
                Journal ID (iso-abbrev): Nat. Methods
                Title: Nature methods
                ISSN (Print): 1548-7091
                ISSN (Electronic): 1548-7105
                Publication date Nihms-submitted: 29 July 2015
                Publication date (Electronic): 17 August 2015
                Publication date (Print): October 2015
                Publication date PMC-release: 01 April 2016
                Volume: 12
                Issue: 10
                Pages: 943-946
                Affiliations
                [1 ]Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA USA
                [2 ]Graduate Group in Biophysics, University of California, San Francisco, CA USA
                [3 ]Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
                [4 ]Graduate program in Biological Physics, Structure and Design, University of Washington, Seattle, WA USA
                [5 ]Department of Biochemistry, University of Washington, Seattle, WA USA
                [6 ]Keck Advanced Microscopy Laboratory, Department of Biochemistry and Biophysics, University of California, San Francisco, CA USA
                [7 ]Institute for Protein Design, Seattle, WA USA
                [8 ]Department of Bioengineering, University of California Berkeley, Berkeley, CA USA
                Author notes
                Article
                Manuscript ID: NIHMS710817
                DOI: 10.1038/nmeth.3541
                PMC ID: 4589481
                PubMed ID: 26280328
                SO-VID: 0c0dcb2e-e5d0-4fd5-a9e3-f1692f4c871f
                License:

                Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use: http://www.nature.com/authors/editorial_policies/license.html#terms

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                ScienceOpen disciplines: Life sciences

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