Letter | Published:

Cryo-EM reveals a novel octameric integrase structure for betaretroviral intasome function

Nature volume 530, pages 358361 (18 February 2016) | Download Citation


Retroviral integrase catalyses the integration of viral DNA into host target DNA, which is an essential step in the life cycle of all retroviruses1. Previous structural characterization of integrase–viral DNA complexes, or intasomes, from the spumavirus prototype foamy virus revealed a functional integrase tetramer2,3,4,5, and it is generally believed that intasomes derived from other retroviral genera use tetrameric integrase6,7,8,9. However, the intasomes of orthoretroviruses, which include all known pathogenic species, have not been characterized structurally. Here, using single-particle cryo-electron microscopy and X-ray crystallography, we determine an unexpected octameric integrase architecture for the intasome of the betaretrovirus mouse mammary tumour virus. The structure is composed of two core integrase dimers, which interact with the viral DNA ends and structurally mimic the integrase tetramer of prototype foamy virus, and two flanking integrase dimers that engage the core structure via their integrase carboxy-terminal domains. Contrary to the belief that tetrameric integrase components are sufficient to catalyse integration, the flanking integrase dimers were necessary for mouse mammary tumour virus integrase activity. The integrase octamer solves a conundrum for betaretroviruses as well as alpharetroviruses by providing critical carboxy-terminal domains to the intasome core that cannot be provided in cis because of evolutionarily restrictive catalytic core domain–carboxy-terminal domain linker regions. The octameric architecture of the intasome of mouse mammary tumour virus provides new insight into the structural basis of retroviral DNA integration.

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Primary accessions

Electron Microscopy Data Bank

Data deposits

Coordinates of cryo-EM density maps for the full and core intasome datasets have been deposited in the Electron Microscopy Data Bank under accession numbers EMD-6440 and EMD-6441, respectively. X-ray diffraction data and the resulting INCCD, INNTD–CCD and INCTD structures have been deposited in the Protein Data Bank (PDB) under accession numbers 5CZ1, 5CZ2 and 5D7U, respectively. The core intasome structure has been deposited in the Protein Data Bank under accession number 3JCA.


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We acknowledge support from US National Institutes of Health (NIH) grants R01 AI070042 (to A.N.E.), NIH P50 GM103368 and the Leona M. and Harry B. Helmsley Charitable Trust grant number 2012-PG-MED002 (to D.L., both funding sources provided equal support), NIH P50 GM082251 (to P.C.), NIH P30 AI060354 (Harvard University Center for AIDS Research), and US National Science Foundation grants NSF-ACI-1339649 and TG-MCB070039 (to B.D.). B.D. acknowledges support from San Antonio Cancer Institute grant CA054174 for the Center for Analytical Ultracentrifugation of Macromolecular Assemblies at the University of Texas Health Science Center at San Antonio. Molecular graphics and analyses were performed with the USCF Chimera package (supported by NIH P41 GM103331). CryoEM data collection was in part facilitated by the National Resource for Automated Molecular Microscopy (9 P41 GM103310). We thank B. Anderson and J.-C. Ducom at The Scripps Research Institute for help with EM data collection and network infrastructure, J. Fitzpatrick and F. Dwyer for computational support at The Salk Institute, V. Pye for help with X-ray structure refinement and the staff of BM14 (European Synchrotron Radiation Facility, Grenoble, France) and I03 (Diamond Light Source, Oxfordshire, UK) beamlines for assistance with data collection.

Author information


  1. Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute and Department of Medicine, Harvard Medical School, 450 Brookline Avenue, Boston, Massachusetts 02215, USA

    • Allison Ballandras-Colas
    • , Tamaria G. Dewdney
    •  & Alan N. Engelman
  2. Laboratory of Genetics and Helmsley Center for Genomic Medicine, The Salk Institute for Biological Studies, 10010 N Torrey Pines Road, La Jolla, California 92037, USA

    • Monica Brown
    •  & Dmitry Lyumkis
  3. Clare Hall Laboratories, The Francis Crick Institute, Blanche Lane, South Mimms, Potters Bar, Hertfordshire EN6 3LD, UK

    • Nicola J. Cook
    •  & Peter Cherepanov
  4. Department of Biochemistry, The University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, Texas 78229, USA

    • Borries Demeler
  5. Division of Medicine, Imperial College London, St. Mary’s Campus, Norfolk Place, London W2 1PG, UK

    • Peter Cherepanov


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A.B.-C. and A.N.E. discovered how to assemble MMTV intasomes; A.B.-C. and T.G.D. expressed and purified MMTV IN proteins for biochemical analysis; A.B.-C. assembled intasomes, characterized their biochemistry, supplied them for cryo-EM and centrifugation analyses, and performed IN activity assays; M.B. and D.L. performed EM work, collected cryo-EM data and determined the structure; D.L. modelled the intasome structure; B.D. collected and analysed the sedimentation velocity data; N.J.C. and P.C. expressed and purified INCCD, INNTD–CCD and INCTD/212–266 constructs, established crystallization conditions and determined these structures.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Dmitry Lyumkis or Alan N. Engelman.

Extended data

Supplementary information

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  1. 1.

    Supplementary Information

    This file contains Supplementary Figure 1 – source data gels for Figures 1c and 4a.


  1. 1.

    Catalytic core domain in segmented electron density map

    Catalytic core domain in segmented electron density map

  2. 2.

    N-terminal domain in segmented electron density map

    N-terminal domain in segmented electron density map

  3. 3.

    C-terminal domain in segmented electron density map

    C-terminal domain in segmented electron density map.

  4. 4.

    Viral DNA in segmented electron density map

    Viral DNA in segmented electron density map.

  5. 5.

    MMTV intasome structure in electron density map with close up views of NTD1-CCD1, CCD1-CTD1 and CCD2-CTD2 linker regions

    MMTV intasome structure in electron density map with close up views of NTD1-CCD1, CCD1-CTD1 and CCD2-CTD2 linker regions

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