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Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics

Nature volume 497, pages 643–646 (2013)Cite this article

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Abstract

Retroviral capsid proteins are conserved structurally but assemble into different morphologies1. The mature human immunodeficiency virus-1 (HIV-1) capsid is best described by a ‘fullerene cone’ model2,3, in which hexamers of the capsid protein are linked to form a hexagonal surface lattice that is closed by incorporating 12 capsid-protein pentamers. HIV-1 capsid protein contains an amino-terminal domain (NTD) comprising seven α-helices and a β-hairpin4,5, a carboxy-terminal domain (CTD) comprising four α-helices6,7, and a flexible linker with a 310-helix connecting the two structural domains8. Structures of the capsid-protein assembly units have been determined by X-ray crystallography9,10; however, structural information regarding the assembled capsid and the contacts between the assembly units is incomplete. Here we report the cryo-electron microscopy structure of a tubular HIV-1 capsid-protein assembly at 8 Å resolution and the three-dimensional structure of a native HIV-1 core by cryo-electron tomography. The structure of the tubular assembly shows, at the three-fold interface11, a three-helix bundle with critical hydrophobic interactions. Mutagenesis studies confirm that hydrophobic residues in the centre of the three-helix bundle are crucial for capsid assembly and stability, and for viral infectivity. The cryo-electron-microscopy structures enable modelling by large-scale molecular dynamics simulation, resulting in all-atom models for the hexamer-of-hexamer and pentamer-of-hexamer elements as well as for the entire capsid. Incorporation of pentamers results in closer trimer contacts and induces acute surface curvature. The complete atomic HIV-1 capsid model provides a platform for further studies of capsid function and for targeted pharmacological intervention.

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Figure 1: Cryo-EM reconstruction of HIV-1 CA tubular assembly at 8 Å resolution and MDFF.
Figure 2: Mutational analysis of the hydrophobic trimer interface.
Figure 3: All-atom molecular dynamics simulation of CA tubular assembly.
Figure 4: All-atom HIV-1 capsid model.

Accession codes

Accessions

Protein Data Bank

Data deposits

Cryo-EM structural data have been deposited in the EMDataBank under accession codesEMD-5582 andEMD-5639, and the MDFF atomic model of the CA HOH and models of HIV-1 capsid have been deposited in the Protein Data Bank under accession numbers 3J34, 3J3Q, 3J3Y.

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Acknowledgements

We thank P. Schwerdtfeger for access to his software for creating fullerene models, T. Brosenitsch for reading the manuscript, and M. DeLucia and J. Mehrens for technical assistance. This work was supported by the National Institutes of Health (GM082251, GM085043 and GM104601) and the National Science Foundation (PHY0822613, MCB0744057). Large-scale molecular dynamics simulations were performed on the Blue Waters Computer, financed by the National Science Foundation (OCI 07-25070).

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Author notes

  1. Gongpu Zhao, Juan R. Perilla and Ernest L. Yufenyuy: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, 15260, Pennsylvania, USA

    Gongpu Zhao, Xin Meng, Jiying Ning, Jinwoo Ahn, Angela M. Gronenborn & Peijun Zhang

  2. Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, Pittsburgh, 15260, Pennsylvania, USA

    Gongpu Zhao, Ernest L. Yufenyuy, Xin Meng, Jiying Ning, Jinwoo Ahn, Angela M. Gronenborn, Christopher Aiken & Peijun Zhang

  3. Department of Physics and Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, 61801, Illinois, USA

    Juan R. Perilla & Klaus Schulten

  4. Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, 37232, Tennessee, USA

    Ernest L. Yufenyuy & Christopher Aiken

  5. Department of Physics, University of Central Florida, Orlando, 32816, Florida, USA

    Bo Chen

  6. Department of Mechanical Engineering and Materials Science, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, 15260, Pennsylvania, USA

    Peijun Zhang

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Contributions

G.Z., J.R.P., E.L.Y., A.M.G., K.S., C.A. and P.Z. designed the research. J.N. and J.A. prepared samples for electron microscopy. G.Z. collected cryo-EM data. G.Z., X.M. and P.Z. analysed cryo-EM and cryo-ET data. E.L.Y. and C.A. performed biochemical and functional analysis. K.S. developed large-scale modelling methodology; J.R.P. performed molecular dynamics simulations and B.C. performed CG-MC simulations. G.Z., J.R.P., K.S. and P.Z. analysed atomic models. G.Z., J.R.P., A.M.G., K.S., C.A. and P.Z wrote the paper with support from all the authors.

Corresponding authors

Correspondence to Klaus Schulten, Christopher Aiken or Peijun Zhang.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file contains Supplementary Methods, Supplementary Table 1, Supplementary Figures 1-8 and Supplementary References. (PDF 7830 kb)

Molecular dynamics flexible fitting of CA assembly

Helvetica (MOV 6358 kb)

Molecular dynamics simulation of HIV-1 CA pentamer of hexamers

Molecular dynamics simulation of the transition from a relatively flat conformation of a pentamer of hexamers (POH), to a dome-like shape conformation during 300ns. The central pentamer is shown in orange, the surrounding five hexamers are shown in gray. Residues Tyr 184 and Met 185 are shown in spherical representation. (MOV 22123 kb)

Fully equilibrated HIV-1 CA pentamer of hexamers model

Equilibrated structure of the pentamer of hexamers model (POH) in surface representation after 400ns molecular dynamics simulation. The CTDs from both pentamers and hexamers are shown in orange; NTDs belonging to the hexamers are colored in blue, while its pentamer counterpart is shown in green. (MOV 2776 kb)

Cryo-electron tomographic reconstruction of a native HIV-1 core

Computational slices through the 3D tomographic volume of a native HIV-1 core. (MOV 314 kb)

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Zhao, G., Perilla, J., Yufenyuy, E. et al. Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics. Nature 497, 643–646 (2013). https://doi.org/10.1038/nature12162

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