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

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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

1. Glockshuber R et al
(2020) 3.5 Å cryoSPARC map
EMDB, EMD-11388.

http://www.ebi.ac.uk/pdbe/entry/emdb/EMD-11388
1. Glockshuber R et al
(2020) UMOD AU model
PDB, 6ZS5.

http://www.rcsb.org/structure/6ZS5
1. Glockshuber R et al
(2020) longated model of UMOD filament derived from cryoSPARC map
PDB, 6ZYA.

http://www.rcsb.org/structure/6ZYA
1. Glockshuber R et al
(2020) Å cisTEM map
EMDB, EMD-11471.

http://www.ebi.ac.uk/pdbe/entry/emdb/EMD-11471

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.

https://gnomad.broadinstitute.org/

Article and author information

Author details

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.

"This ORCID iD identifies the author of this article:" 0000-0002-2702-8092
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.

"This ORCID iD identifies the author of this article:" 0000-0001-8471-469X
Pavel Afanasyev

Cryo-EM Knowledge Hub (CEMK), Swiss Federal Institute of Technology, Zurich, Switzerland

Competing interests
The authors declare that no competing interests exist.
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.
Anne Kipp

Institute of Physiology, University of Zurich, Zurich, Switzerland

Competing interests
The authors declare that no competing interests exist.
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.

"This ORCID iD identifies the author of this article:" 0000-0003-1178-7980
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.

"This ORCID iD identifies the author of this article:" 0000-0003-3744-4767
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.

"This ORCID iD identifies the author of this article:" 0000-0002-3649-3340
Daniel Boehringer

Institute for Molecular Biology and Biophysics, ETH Zürich, Zürich, Switzerland

Competing interests
The authors declare that no competing interests exist.
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.

"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.

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.

Copyright

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.