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Novel fold and capsid-binding properties of the λ-phage display platform protein gpD

Nature Structural Biology volume 7, pages 230–237 (2000)Cite this article

Abstract

The crystal structure of gpD, the capsid-stabilizing protein of bacteriophage λ, was solved at 1.1 Å resolution. Data were obtained from twinned crystals in space group P21 and refined with anisotropic temperature factors to an R-factor of 0.098 (Rfree = 0.132). GpD (109 residues) has a novel fold with an unusually low content of regular secondary structure. Noncrystallographic trimers with substantial intersubunit interfaces were observed. The C-termini are well ordered and located on one side of the trimer, relatively far from its three-fold axis. The N-termini are disordered up to Ser 15, which is close to the three-fold axis and on the same side as the C-termini. A density map of the icosahedral viral capsid at 15 Å resolution, obtained by cryo-electron microscopy and image reconstruction, reveals gpD trimers, seemingly indistinguishable from the ones seen in the crystals, at all three-fold sites. The map further reveals that the side of the trimer that binds to the capsid is the side on which both termini reside. Despite this orientation of the gpD trimer, fusion proteins connected by linker peptides to either terminus bind to the capsid, allowing protein and peptide display.

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Figure 1: Electron density maps for gpD.
Figure 2: Stereo view of the structure of the gpD monomer.
Figure 3: Primary and secondary structures of gpD.
Figure 4: Stereo view of the gpD trimer viewed from the bottom side.
Figure 5: The molecular surface of the gpD trimer.
Figure 6: Electron micrographs of phage λ capsids.
Figure 7: Modeling of the crystal structure of the gpD trimer (red) into the portion of the cryo-EM density map (blue) that represents the gpD trimer at the three-fold axis of symmetry.

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Acknowledgements

We thank V. Hawkins for assistance with the capsid preparations, H. Iwai and O. Zerbe for performing the NMR experiments and for stimulating discussions, M. Feiss, R. Weisberg, D. Belnap, and R. Hendrix for helpful suggestions, M. Feiss and R. Hoess for supplying material, and A. Arthur for editorial comments.

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Author notes

  1. James F. Conway

    Present address: Institut de Biologie Structurale, 41 rue Jules Horowitz, 38027, Grenoble, Cedex 1, France

  2. Fan Yang, Patrik Forrer, James F. Conway, Naiqian Cheng, Mario E. Cerritelli and Alasdair C. Steven: These authors contributed equally to this work.

Authors and Affiliations

  1. Macromolecular Crystallography Laboratory, Program in Structural Biology, National Cancer Institute, Frederick Cancer Research and Development Center, Frederick, 21702, Maryland, USA

    Fan Yang & Alexander Wlodawer

  2. Biochemisches Institut, Universität Zürich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland

    Patrik Forrer & Andreas Plückthun

  3. NCI-FCRDC and NSLS, Brookhaven National Laboratory, Bldg. 725A-X9, Upton, 11973, New York, USA

    Zbigniew Dauter

  4. Laboratory of Structural Biology, National Institute of Arthritis, and Musculoskeletal and Skin Diseases, Bethesda, 20892, Maryland, USA

    James F. Conway, Naiqian Cheng, Mario E. Cerritelli & Alasdair C. Steven

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Correspondence to Andreas Plückthun.

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Yang, F., Forrer, P., Dauter, Z. et al. Novel fold and capsid-binding properties of the λ-phage display platform protein gpD. Nat Struct Mol Biol 7, 230–237 (2000). https://doi.org/10.1038/73347

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