CryoEM structures of membrane pore and prepore complex reveal cytolytic mechanism of Pneumolysin

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Abstract

Many pathogenic bacteria produce pore-forming toxins to attack and kill human cells. We have determined the 4.5 Å structure of the ~2.2 MDa pore complex of pneumolysin, the main virulence factor of Streptococcus pneumoniae, by cryoEM. The pneumolysin pore is a 400 Å ring of 42 membrane-inserted monomers. Domain D3 of the soluble toxin refolds into two ~85 Å β-hairpins that traverse the lipid bilayer and assemble into a 168-strand β-barrel. The pore complex is stabilized by salt bridges between β-hairpins of adjacent subunits and an internal α-barrel. The apolar outer barrel surface with large sidechains is immersed in the lipid bilayer, while the inner barrel surface is highly charged. Comparison of the cryoEM pore complex to the prepore structure obtained by electron cryo-tomography and the x-ray structure of the soluble form reveals the detailed mechanisms by which the toxin monomers insert into the lipid bilayer to perforate the target membrane.

Data availability

The following data sets were generated

1. van Pee K
2. Yildiz O
(2016) Crystal structure of pneumolysin D168A mutant
Publicly available at the RCSB Protein Data Bank (accession no: 5AOE).

http://www.rcsb.org/pdb/explore/explore.do?structureId=5AOE
1. van Pee K
2. Yildiz O
(2016) Crystal structure of pneumolysin deletion mutant Delta146_147
Publicly available at the RCSB Protein Data Bank (accession no: 5AOF).

http://www.rcsb.org/pdb/explore/explore.do?structureId=5AOF
1. van Pee K
2. Neuhaus A
3. D'Imprima E
4. Mills DJ
5. Kuehlbrandt
6. W
7. Yildiz O
(2016) CryoEM structure of the membrane pore complex of Pneumolysin at 4.5A
Publicly available at the EMBL-EBI Protein Data Bank (accession no: 5LY6).

https://www.ebi.ac.uk/pdbe/entry/pdb/5ly6
1. van Pee K
2. Neuhaus A
3. D'Imprima E
4. Mills DJ
5. Kuehlbrandt
6. W
7. Yildiz O
(2016) CryoEM structure of the membrane pore complex of Pneumolysin at 4.5A
Publicly available at the EMBL-EBI Protein Data Bank (accession no: EMD-4118).

http://www.ebi.ac.uk/pdbe/entry/emdb/EMD-4118

The following previously published data sets were used

1. van Pee K
2. Yildiz O
(2015) Crystal structure of wild type pneumolysin.
Publicly available at the RCSB Protein Data Bank (accession no: 5AOD).

http://www.rcsb.org/pdb/explore/explore.do?structureId=5aod

Article and author information

Author details

Katharina van Pee

Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany

Competing interests
No competing interests declared.
Alexander Neuhaus

Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany

Competing interests
No competing interests declared.
Edoardo D'Imprima

Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany

Competing interests
No competing interests declared.
Deryck J Mills

Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany

Competing interests
No competing interests declared.
Werner Kühlbrandt

Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany

For correspondence
werner.kuehlbrandt@biophys.mpg.de

Competing interests
Werner Kühlbrandt, Reviewing editor, eLife.

"This ORCID iD identifies the author of this article:" 0000-0002-2013-4810
Özkan Yildiz

Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany

For correspondence
Oezkan.Yildiz@biophys.mpg.de

Competing interests
No competing interests declared.

"This ORCID iD identifies the author of this article:" 0000-0003-3659-2805

Funding

Max-Planck-Gesellschaft (DepartmentSB)

Katharina van Pee
Alexander Neuhaus
Edoardo D'Imprima
Deryck J Mills
Werner Kühlbrandt
Özkan Yildiz

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

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.