The cryo-EM structure of the human uromodulin filament core reveals a unique assembly mechanism

  1. Jessica J Stanisich
  2. Dawid S Zyla
  3. Pavel Afanasyev
  4. Jingwei Xu
  5. Anne Kipp
  6. Eric Olinger
  7. Olivier Devuyst
  8. Martin Pilhofer
  9. Daniel Boehringer
  10. Rudi Glockshuber  Is a corresponding author
  1. Institute of Molecular Biology and Biophysics, Swiss Federal Institute of Technology, Switzerland
  2. Swiss Federal Institute of Technology, Switzerland
  3. University of Zurich, Switzerland
  4. Newcastle University, United Kingdom
  5. ETH Zürich, Switzerland

Abstract

The glycoprotein uromodulin (UMOD) is the most abundant protein in human urine and forms filamentous homopolymers that encapsulate and aggregate uropathogens, promoting pathogen clearance by urine excretion. Despite its critical role in the innate immune response against urinary tract infections, the structural basis and mechanism of UMOD polymerization remained unknown. Here, we present the cryo-EM structure of the UMOD filament core at 3.5 Å resolution, comprised of the bipartite zona pellucida (ZP) module in a helical arrangement with a rise of ~65 Å and a twist of ~180°. The immunoglobulin-like ZPN and ZPC subdomains of each monomer are separated by a long linker that interacts with the preceding ZPC and following ZPN subdomains by β-sheet complementation. The unique filament architecture suggests an assembly mechanism in which subunit incorporation could be synchronized with proteolytic cleavage of the C-terminal pro-peptide that anchors assembly-incompetent UMOD precursors to the membrane.

Data availability

Structures and maps presented in this paper have been deposited to the Protein Data Bank (PDB) and Electron Microscopy Data Base (EMDB) with the following accession codes: 3.5 Å cryoSPARC map EMD-11388, the UMOD AU model PDB ID: 6ZS5, elongated model of UMOD filament derived from cryoSPARC map PDB ID: 6ZYA, 4.7 Å cisTEM map EMD-11471.

The following data sets were generated
The following previously published data sets were used
    1. Karczewski KJ et al
    (2020) Genome Aggregation Database (GnomAD)
    Genome Aggregation Database (GnomAD) v2.1.1, GRCh37.

Article and author information

Author details

  1. Jessica J Stanisich

    Biology, Institute of Molecular Biology and Biophysics, Swiss Federal Institute of Technology, Zurich, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2702-8092
  2. Dawid S Zyla

    Biology, Institute of Molecular Biology and Biophysics, Swiss Federal Institute of Technology, Zurich, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-8471-469X
  3. Pavel Afanasyev

    Cryo-EM Knowledge Hub (CEMK), Swiss Federal Institute of Technology, Zurich, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
  4. Jingwei Xu

    Biology, Institute of Molecular Biology and Biophysics, Swiss Federal Institute of Technology, Zurich, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
  5. Anne Kipp

    Institute of Physiology, University of Zurich, Zurich, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
  6. Eric Olinger

    Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1178-7980
  7. Olivier Devuyst

    Institute of Physiology, Zurich Center for Integrative Human Physiology, University of Zurich, Zurich, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-3744-4767
  8. Martin Pilhofer

    Biology, Institute of Molecular Biology and Biophysics, Swiss Federal Institute of Technology, Zurich, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-3649-3340
  9. Daniel Boehringer

    Institute for Molecular Biology and Biophysics, ETH Zürich, Zürich, Switzerland
    Competing interests
    The authors declare that no competing interests exist.
  10. Rudi Glockshuber

    Biology, Institute of Molecular Biology and Biophysics, Swiss Federal Institute of Technology, Zurich, Switzerland
    For correspondence
    rudi@mol.biol.ethz.ch
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-3320-3843

Funding

Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (310030B_176403/1)

  • Rudi Glockshuber

Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (31003A_156304)

  • Rudi Glockshuber

Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (31003A_179255)

  • Martin Pilhofer

H2020 European Research Council (679209)

  • Martin Pilhofer

NOMIS Stiftung (n/a)

  • Martin Pilhofer

Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (310030_189044)

  • Olivier Devuyst

Swiss National Centre of Competence in Research Kidney Control of Homeostasis (n/a)

  • Olivier Devuyst

Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (P2ZHP3_195181)

  • Eric Olinger

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

Reviewing Editor

  1. Sjors HW Scheres, MRC Laboratory of Molecular Biology, United Kingdom

Ethics

Human subjects: The use of human urine samples for UMOD purification was approved by the Ethical Committee of the UCLouvain Medical School in Brussels, Belgium (Project EUNEFRON, 2011/04May/184). All individuals gave written informed consent.The completed "Consent form for publication in eLife" has been filed on the donor's behalf.

Version history

  1. Received: June 22, 2020
  2. Accepted: August 19, 2020
  3. Accepted Manuscript published: August 20, 2020 (version 1)
  4. Version of Record published: September 11, 2020 (version 2)

Copyright

© 2020, Stanisich 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.

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  1. Jessica J Stanisich
  2. Dawid S Zyla
  3. Pavel Afanasyev
  4. Jingwei Xu
  5. Anne Kipp
  6. Eric Olinger
  7. Olivier Devuyst
  8. Martin Pilhofer
  9. Daniel Boehringer
  10. Rudi Glockshuber
(2020)
The cryo-EM structure of the human uromodulin filament core reveals a unique assembly mechanism
eLife 9:e60265.
https://doi.org/10.7554/eLife.60265

Share this article

https://doi.org/10.7554/eLife.60265

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