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Structure of a KirBac potassium channel with an open bundle crossing indicates a mechanism of channel gating

Nature Structural & Molecular Biology volume 19, pages 158–163 (2012)Cite this article

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Abstract

KirBac channels are prokaryotic homologs of mammalian inwardly rectifying (Kir) potassium channels, and recent crystal structures of both Kir and KirBac channels have provided major insight into their unique structural architecture. However, all of the available structures are closed at the helix bundle crossing, and therefore the structural mechanisms that control opening of their primary activation gate remain unknown. In this study, we engineered the inner pore-lining helix (TM2) of KirBac3.1 to trap the bundle crossing in an apparently open conformation and determined the crystal structure of this mutant channel to 3.05 Å resolution. Contrary to previous speculation, this new structure suggests a mechanistic model in which rotational 'twist' of the cytoplasmic domain is coupled to opening of the bundle-crossing gate through a network of inter- and intrasubunit interactions that involve the TM2 C-linker, slide helix, G-loop and the CD loop.

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Figure 1: Structure of the KirBac3.1 S129R mutant in an apparently open conformation.
Figure 2: Bending of the inner TM2 helices during channel opening.
Figure 3: KirBac3.1 S129R is in a twisted yet conductive conformation.
Figure 4: Interaction network between the CTD and the TMD.

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Acknowledgements

We thank the staff at the I24 beamline at the Diamond Light Source. This work was supported by the Biotechnology and Biological Sciences Research Council and the Wellcome Trust. R. DeZ was supported by a Marie Curie Intra-European Fellowship.

Author information

Author notes

  1. Vassiliy N Bavro & Catherine Vénien-Bryan

    Present address: Present Address: School of Immunity and Infection, University of Birmingham, Birmingham UK (V.N.B.); Institut de Minéralogie et de Physique des Milieux Condensés, Université Pierre et Marie Curie, Centre National de la Recherche Scientifique, UMR 7590, Paris, France (C.V.-B.).,

  2. Vassiliy N Bavro and Rita De Zorzi: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Physics, Clarendon Laboratory, University of Oxford, Oxford, UK

    Vassiliy N Bavro, Matthias R Schmidt, Lejla Zubcevic & Stephen J Tucker

  2. Department of Biochemistry, Laboratory of Molecular Biophysics, University of Oxford, Oxford, UK

    Rita De Zorzi & Catherine Vénien-Bryan

  3. Department of Biochemistry, Structural Bioinformatics and Computational Biochemistry Unit, University of Oxford, Oxford, UK

    Matthias R Schmidt & Mark S P Sansom

  4. Structural Genomics Consortium, University of Oxford, Oxford, UK

    João R C Muniz

  5. OXION Ion Channel Initiative, University of Oxford, Oxford, UK

    Mark S P Sansom, Catherine Vénien-Bryan & Stephen J Tucker

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Contributions

S.J.T. and C.V.-B. conceived and designed the research. R. De Z. and V.N.B. expressed and crystallized the mutant protein. V.N.B., R. De Z. and L.Z. collected the diffraction data. V.N.B. and J.R.C.M. determined and refined the structure with contribution from R. De Z., V.N.B., L.Z. and M.R.S. analyzed and interpreted the structure. L.Z. conducted complementation studies. C.V.-B., M.S.P.S. and S.J.T. supervised the project. V.N.B. and S.J.T. wrote the manuscript with the help of comments from all authors.

Corresponding authors

Correspondence to Catherine Vénien-Bryan or Stephen J Tucker.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–6 (PDF 1440 kb)

Supplementary Movie 1

Opening of the bundle-crossing. Linear interpolation between the non-twist closed state (PDB 2WLJ) to the intermediate twist closed state (PDB 2X6C) and finally to the new, twisted S129R open conformation (PDB 3ZRS). For clarity of presentation, missing residues in the extracellular loops of 2X6C and the βL-M loop of 3ZRS were modelled in. (MOV 2508 kb)

Supplementary Movie 2

Network of Interactions. View of the network of interactions that connects the slide-helix and C-linker to the CD-loop and G-loops on the intracellular assembly. Arg137 on the C-linker and Arg-167 on the CD-loop are critical to integration of this network and may play a key role in controlling the position of the C-linker relative to the CTD. (MOV 5667 kb)

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Bavro, V., De Zorzi, R., Schmidt, M. et al. Structure of a KirBac potassium channel with an open bundle crossing indicates a mechanism of channel gating. Nat Struct Mol Biol 19, 158–163 (2012). https://doi.org/10.1038/nsmb.2208

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