Surface of bacteriorhodopsin revealed by high-resolution electron crystallography

ABSTRACT Bacteriorhodopsin is a transmembrane protein that uses light energy, absorbed by its chromophore retinal, to pump protons from the cytoplasm of bacteria such as _Halobacterium

salinarium_ into the extracellular space1,2. It is made up of seven α-helices, and in the bacterium forms natural, two-dimensional crystals called purple membranes. We have analysed these

crystals by electron cryo-microscopy to obtain images of bacteriorhodopsin at 3.0 å resolution. The structure covers nearly all 248 amino acids, including loops outside the membrane, and

reveals the distribution of charged residues on both sides of the membrane surface. In addition, analysis of the electron-potential map produced by this method allows the determination of

the charge status of these residues. On the extracellular side, four glutamate residues surround the entrance to the proton channel, whereas on the cytoplasmic side, four aspartic acids

occur in a plane at the boundary of the hydrophobic–hydrophilic interface. The negative charges produced by these aspartate residues is encircled by areas of positive charge that may

facilitate accumulation and lateral movement of protons on this surface. Access through your institution Buy or subscribe This is a preview of subscription content, access via your

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* Learn about institutional subscriptions * Read our FAQs * Contact customer support SIMILAR CONTENT BEING VIEWED BY OTHERS STRUCTURAL BASIS FOR THE PROLONGED PHOTOCYCLE OF SENSORY RHODOPSIN

II REVEALED BY SERIAL SYNCHROTRON CRYSTALLOGRAPHY Article Open access 11 April 2025 MECHANISMS OF INWARD TRANSMEMBRANE PROTON TRANSLOCATION Article 29 June 2023 CRYO-EM STRUCTURE AND

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Scholar  Download references ACKNOWLEDGEMENTS We thank M. Ikehara for encouragement and support; W. Kühlbrandt and D. N. Wang for help with data processing; R. Henderson, S. Fuller, J.

Lanyi, W. Stoeckenius, Y. Harada and J.Sasaki for helpful discussions; T. Miyata for preparing this manuscript; and Digital Equipment Corporation for help with computers. AUTHOR INFORMATION

Author notes * Yoshinori Fujiyoshi Present address: Department of Biophysics, Faculty of Science, Kyoto University, Oiwake Kitashirakawa, Sakyou-ku, 606-01, Kyoto, Japan * Dmitry G.

Vassylyev Present address: International Institute for Advanced Research (IIAR), Matsushita Electric Industrial Co., Ltd., 3-4 Hikaridai, Seika, Soraku, Kyoto, 619-02, Japan * Atsuo Miyazawa

Present address: MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 2QH, UK * Akinori Kidera Present address: Department of Chemistry, Faculty of Science, Kyoto University,

Oiwake Kitashirakawa, Sakyou-ku, Kyoto, 606-01, Japan AUTHORS AND AFFILIATIONS * Biomolecular Engineering Research Institute (formerly Protein Engineering Institute), 6-2-3 Fureudai, Suita,

565, Osaka, Japan Yoshiaki Kimura, Dmitry G. Vassylyev, Atsuo Miyazawa & Akinori Kidera * Rational Drug Design Laboratory, 4-1-4 Misato, Matsukawa, 960-12, Fukushima, Japan Masaaki

Matsushima * International Institute for Advanced Research, Matsushita Electric Industrial Co., 3-4 Hikaridai, Seika, Soraku, 619-02, Kyoto, Japan Kaoru Mitsuoka, Kazuyoshi Murata, Teruhisa

Hirai & Yoshinori Fujiyoshi * Department of Biophysics, Faculty of Science, Kyoto University, Oiwake Kitashirakawa, Sakyou-ku, 606-01, Kyoto, Japan Dmitry G. Vassylyev, Atsuo Miyazawa 

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author inPubMed Google Scholar CORRESPONDING AUTHOR Correspondence to Yoshiaki Kimura. RIGHTS AND PERMISSIONS Reprints and permissions ABOUT THIS ARTICLE CITE THIS ARTICLE Kimura, Y.,

Vassylyev, D., Miyazawa, A. _et al._ Surface of bacteriorhodopsin revealed by high-resolution electron crystallography. _Nature_ 389, 206–211 (1997). https://doi.org/10.1038/38323 Download

citation * Received: 21 October 1996 * Accepted: 02 June 1997 * Issue Date: 11 September 1997 * DOI: https://doi.org/10.1038/38323 SHARE THIS ARTICLE Anyone you share the following link with

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