Importin-9 wraps around the H2A-H2B core to act as nuclear importer and histone chaperone

  1. Abhilash Padavannil
  2. Prithwijit Sarkar
  3. Seung Joong Kim
  4. Tolga Cagatay
  5. Jenny Jiou
  6. Chad A Brautigam
  7. Diana R Tomchick
  8. Andrej Sali
  9. Sheena D'Arcy
  10. Yuh Min Chook  Is a corresponding author
  1. University of Texas Southwestern Medical Center, United States
  2. University of Texas at Dallas, United States
  3. Korea Advanced Institute of Science and Technology (KAIST), Korea (South), Republic of
  4. University of California, San Francisco, United States

Abstract

We report the crystal structure of nuclear import receptor Importin-9 bound to its cargo, the histones H2A-H2B. Importin-9 wraps around the core, globular region of H2A-H2B to form an extensive interface. The nature of this interface coupled with quantitative analysis of deletion mutants of H2A-H2B suggest that the NLS-like sequences in the H2A-H2B tails play a minor role in import. Importin-9•H2A-H2B is reminiscent of interactions between histones and histone chaperones in that it precludes H2A-H2B interactions with DNA and H3-H4 as seen in the nucleosome. Like many histone chaperones, which prevent inappropriate non-nucleosomal interactions, Importin-9 also sequesters H2A-H2B from DNA. Importin-9 appears to act as a storage chaperone for H2A-H2B while escorting it to the nucleus. Surprisingly, RanGTP does not dissociate Importin-9•H2A-H2B but assembles into a RanGTP•Importin-9•H2A-H2B complex. The presence of Ran in the complex, however, modulates Imp9-H2A-H2B interactions to facilitate its dissociation by DNA and assembly into a nucleosome.

Data availability

Diffraction data have been deposited in PDB under the accession code 6N1Z

The following data sets were generated

Article and author information

Author details

  1. Abhilash Padavannil

    Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Prithwijit Sarkar

    Department of Biological Sciences, University of Texas at Dallas, Dallas, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Seung Joong Kim

    Department of Physics, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Korea (South), Republic of
    Competing interests
    The authors declare that no competing interests exist.
  4. Tolga Cagatay

    Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Jenny Jiou

    Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Chad A Brautigam

    Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. Diana R Tomchick

    Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7529-4643
  8. Andrej Sali

    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-0435-6197
  9. Sheena D'Arcy

    Department of Chemistry and Biochemistry, University of Texas at Dallas, Dallas, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-5055-988X
  10. Yuh Min Chook

    Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States
    For correspondence
    yuhmin.chook@utsouthwestern.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-4974-0726

Funding

National Institutes of Health

  • Yuh Min Chook

Welch Foundation

  • Yuh Min Chook

Leukemia and Lymphoma Society

  • Yuh Min Chook

National Institutes of Health

  • Abhilash Padavannil
  • Tolga Cagatay
  • Jenny Jiou

National Institutes of Health

  • Chad A Brautigam
  • Diana R Tomchick
  • Andrej Sali

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

© 2019, Padavannil et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 4,711
    views
  • 668
    downloads
  • 51
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Abhilash Padavannil
  2. Prithwijit Sarkar
  3. Seung Joong Kim
  4. Tolga Cagatay
  5. Jenny Jiou
  6. Chad A Brautigam
  7. Diana R Tomchick
  8. Andrej Sali
  9. Sheena D'Arcy
  10. Yuh Min Chook
(2019)
Importin-9 wraps around the H2A-H2B core to act as nuclear importer and histone chaperone
eLife 8:e43630.
https://doi.org/10.7554/eLife.43630

Share this article

https://doi.org/10.7554/eLife.43630

Further reading

    1. Immunology and Inflammation
    2. Structural Biology and Molecular Biophysics
    Colleen A Maillie, Kiana Golden ... Marco Mravic
    Research Article

    A potent class of HIV-1 broadly neutralizing antibodies (bnAbs) targets the envelope glycoprotein’s membrane proximal exposed region (MPER) through a proposed mechanism where hypervariable loops embed into lipid bilayers and engage headgroup moieties alongside the epitope. We address the feasibility and determinant molecular features of this mechanism using multi-scale modeling. All-atom simulations of 4E10, PGZL1, 10E8, and LN01 docked onto HIV-like membranes consistently form phospholipid complexes at key complementarity-determining region loop sites, solidifying that stable and specific lipid interactions anchor bnAbs to membrane surfaces. Ancillary protein-lipid contacts reveal surprising contributions from antibody framework regions. Coarse-grained simulations effectively capture antibodies embedding into membranes. Simulations estimating protein-membrane interaction strength for PGZL1 variants along an inferred maturation pathway show bilayer affinity is evolved and correlates with neutralization potency. The modeling demonstrated here uncovers insights into lipid participation in antibodies’ recognition of membrane proteins and highlights antibody features to prioritize in vaccine design.

    1. Immunology and Inflammation
    2. Structural Biology and Molecular Biophysics
    Ana Cristina Chang-Gonzalez, Aoi Akitsu ... Wonmuk Hwang
    Research Advance

    Increasing evidence suggests that mechanical load on the αβ T-cell receptor (TCR) is crucial for recognizing the antigenic peptide-bound major histocompatibility complex (pMHC) molecule. Our recent all-atom molecular dynamics (MD) simulations revealed that the inter-domain motion of the TCR is responsible for the load-induced catch bond behavior of the TCR-pMHC complex and peptide discrimination (Chang-Gonzalez et al., 2024). To further examine the generality of the mechanism, we perform all-atom MD simulations of the B7 TCR under different conditions for comparison with our previous simulations of the A6 TCR. The two TCRs recognize the same pMHC and have similar interfaces with pMHC in crystal structures. We find that the B7 TCR-pMHC interface stabilizes under ∼15 pN load using a conserved dynamic allostery mechanism that involves the asymmetric motion of the TCR chassis. However, despite forming comparable contacts with pMHC as A6 in the crystal structure, B7 has fewer high-occupancy contacts with pMHC and exhibits higher mechanical compliance during the simulation. These results indicate that the dynamic allostery common to the TCRαβ chassis can amplify slight differences in interfacial contacts into distinctive mechanical responses and nuanced biological outcomes.