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Tubular Crystals and Helical Arrays: Structural Determination of HIV-1 Capsid Assemblies Using Iterative Helical Real-Space Reconstruction

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Electron Crystallography of Soluble and Membrane Proteins

Part of the book series: Methods in Molecular Biology ((MIMB,volume 955))

Abstract

Helical structures are important in many different life forms and are well-suited for structural studies by cryo-EM. A unique feature of helical objects is that a single projection image contains all the views needed to perform a three-dimensional (3D) crystallographic reconstruction. Here, we use HIV-1 capsid assemblies to illustrate the detailed approaches to obtain 3D density maps from helical objects. Mature HIV-1 particles contain a conical- or tubular-shaped capsid that encloses the viral RNA genome and performs essential functions in the virus life cycle. The capsid is composed of capsid protein (CA) oligomers which are helically arranged on the surface. The N-terminal domain (NTD) of CA is connected to its C-terminal domain (CTD) through a flexible hinge. Structural analysis of two- and three-dimensional crystals provided molecular models of the capsid protein (CA) and its oligomer forms. We determined the 3D density map of helically assembled HIV-1 CA hexamers at 16 Å resolution using an iterative helical real-space reconstruction method. Docking of atomic models of CA-NTD and CA-CTD dimer into the electron density map indicated that the CTD dimer interface is retained in the assembled CA. Furthermore, molecular docking revealed an additional, novel CTD trimer interface.

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Acknowledgments

The authors would like to thank Dr. Jinwoo Ahn and Danxia Ke for technical support, and Dr. Teresa Brosenitsch for critical reading of the manuscript. This work was supported by GM082251 and GM085043.

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Authors and Affiliations

  1. Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA

    Peijun Zhang, Xin Meng & Gongpu Zhao

Authors
  1. Peijun Zhang
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  2. Xin Meng
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  3. Gongpu Zhao
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Corresponding author

Correspondence to Peijun Zhang .

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Editors and Affiliations

  1. School of Biology, Georgia Institute of Technology, Ferst Dr. 310, Atlanta, 30332, Georgia, USA

    Ingeborg Schmidt-Krey

  2. , Dept. Biochemistry & Biophysics, University of California, San Francisco, 16th St. 600, San Francisco, 94158, California, USA

    Yifan Cheng

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Zhang, P., Meng, X., Zhao, G. (2013). Tubular Crystals and Helical Arrays: Structural Determination of HIV-1 Capsid Assemblies Using Iterative Helical Real-Space Reconstruction. In: Schmidt-Krey, I., Cheng, Y. (eds) Electron Crystallography of Soluble and Membrane Proteins. Methods in Molecular Biology, vol 955. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-176-9_21

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  • DOI: https://doi.org/10.1007/978-1-62703-176-9_21

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-175-2

  • Online ISBN: 978-1-62703-176-9

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