Exploiting tertiary structure through local folds for crystallographic phasing

Journal name:
Nature Methods
Volume:
10,
Pages:
1099–1101
Year published:
DOI:
doi:10.1038/nmeth.2644
Received
Accepted
Published online
Corrected online

We describe an algorithm for phasing protein crystal X-ray diffraction data that identifies, retrieves, refines and exploits general tertiary structural information from small fragments available in the Protein Data Bank. The algorithm successfully phased, through unspecific molecular replacement combined with density modification, all-helical, mixed alpha-beta, and all-beta protein structures. The method is available as a software implementation: Borges.

At a glance

Figures

  1. Characteristic C[alpha]-O vectors (CVs) used in Borges to handle secondary structure and local fold geometry.
    Figure 1: Characteristic Cα-O vectors (CVs) used in Borges to handle secondary structure and local fold geometry.

    (a) Occurrence of CV values for all β-strands (black) and α-helical (red) tripeptides in the PDB. CVs are shown for each amino acid on a β-strand (left structure) and an α-helix (right structure); the central one highlights the Cα centroid (X(Cα), blue) and O centroid (X(O), red) defining the vector. (b) CV length (CVL) distribution for the fragments displayed. Top, helical structure disrupted by a sharp and a light kink. Center, curved helix showing CVs below the red line representing perfect helicity, consistent with local distortions. Bottom, CVL distribution for the four strands in the β-sheet displayed with colors matching the cartoon plot of the structure at right. Again, distortion brought up by sheet curvature causes a decrease in CV, with the black line representing average CV value for β-strands. Figures were prepared with Gnuplot (http://www.gnuplot.info/) and PyMOL (http://www.pymol.org/).

  2. Overall occurrence of model fragments and their role in phasing an all-beta and a previously unknown structure.
    Figure 2: Overall occurrence of model fragments and their role in phasing an all-beta and a previously unknown structure.

    (a) Solving fragment (green) and SHELXE electron density map (F-weighted mean phase error = 20°) for all-beta 4L1H. (b) Cartoon representation of 4GN0; colored regions display the location of fragments leading to solution. (c) Three of the 13 structures from which models (blue) were extracted to solve the 4GN0 structure: β-catenin–BCL9–Tcf4 complex (2GL7), bacterial Mre11 core (3THN) and cytochrome C nitrite reductase (1QDB). (d) SHELXE electron density map (FwMPE = 42°). The final 4GN0 model is depicted in gray. The closest original fragment (orange) extracted from 2GL7 (ref. 19) has an r.m.s. deviation of 0.90 Å, whereas after refinement (green) the r.m.s. deviation is 0.54 Å.

Accession codes

Primary accessions

Protein Data Bank

Referenced accessions

Protein Data Bank

Swiss-Prot

Change history

Corrected online 05 May 2014
In the version of this article initially published, the authors did not acknowledge all of the people involved in the generation of the crystallographic data set of AF1503 from A. fulgidus. These diffraction data were originated by M. Hulko, A. Ursinus, K. Bär, J. Martin, K.Z. and A.N. Lupas at the Max Planck Institute for Developmental Biology, Tübingen. M. Hulko, A. Ursinus, K. Bär, J. Martin and A.N. Lupas have kindly given their retroactive permission to use the data. Their report on the AF1503 structure was published in the Journal of Structural Biology (doi:10.1016/j.jsb.2014.02.008) and PDB 4CQ4. The error has been corrected in the HTML and PDF versions of the article.

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Author information

Affiliations

  1. Instituto de Biología Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Barcelona, Spain.

    • Massimo Sammito,
    • Claudia Millán,
    • Dayté D Rodríguez,
    • Iñaki M de Ilarduya,
    • Kathrin Meindl,
    • Ivan De Marino,
    • Giovanna Petrillo &
    • Isabel Usón
  2. Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas–Universidad de Salamanca, Salamanca, Spain.

    • Rubén M Buey &
    • José M de Pereda
  3. Ikerbasque Basque Foundation for Science at Unidad de Biofísica, Consejo Superior de Investigaciones Científicas–Universidad del País Vasco, Leioa, Spain.

    • Kornelius Zeth
  4. Lehrstuhl für Strukturchemie, Universität Göttingen, Göttingen, Germany.

    • George M Sheldrick
  5. Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain.

    • Isabel Usón

Contributions

All authors contributed extensively to the work presented in this paper.

Competing financial interests

The authors declare no competing financial interests.

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Supplementary information

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    Supplementary Figures 1 and 2, Supplementary Tables 1 and 2, Supplementary Results and Supplementary Notes 1 and 2

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