Cryo-EM structure of the lysosomal chloride-proton exchanger CLC-7 in complex with OSTM1

Abstract
Data availability
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Abstract

The chloride-proton exchanger CLC-7 plays critical roles in lysosomal homeostasis and bone regeneration and its mutation can lead to osteopetrosis, lysosomal storage disease and neurological disorders. In lysosomes and the ruffled border of osteoclasts, CLC-7 requires a b-subunit, OSTM1, for stability and activity. Here we present electron cryomicroscopy structures of CLC-7 in occluded states by itself and in complex with OSTM1, determined at resolutions up to 2.8 Å. In the complex, the luminal surface of CLC-7 is entirely covered by a dimer of the heavily glycosylated and disulfide-bonded OSTM1, which serves to protect CLC-7 from the degradative environment of the lysosomal lumen. OSTM1 binding does not induce large-scale rearrangements of CLC-7, but does have minor effects the conformation of the ion-conduction pathway, potentially contributing to its regulatory role. These studies provide insights into the role of OSTM1 and serve as a foundation for understanding the mechanisms of CLC-7 regulation.

Data availability

Cryo-EM maps and atomic coordinates have been deposited with the EMDB and PDB under accession codes EMD-22386 and PDB ID 7JM6 for ggCLC-7 and EMD-22389 andPDB ID 7JM7 for human CLC-7/OSTM1. All other reagents are available from the corresponding author upon reasonable request.

The following data sets were generated

1. Schrecker M
2. Hite RK
(2020) Structure of chicken CLC-7
RCSB Protein Data Bank, 7JM6.

https://www.rcsb.org/structure/7JM6
1. Schrecker M
2. Hite RK
(2020) Structure of human CLC-7 in complex with OSTM1
RCSB Protein Data Bank, 7JM7.

https://www.rcsb.org/structure/7JM7
1. Schrecker M
2. Hite RK
(2020) Structure of chicken CLC-7
Electron Microscopy Data Bank, EMD-22386.

https://www.emdataresource.org/EMD-22386
1. Schrecker M
2. Hite RK
(2020) Structure of human CLC-7 in complex with OSTM1
Electron Microscopy Data Bank, EMD-22389.

https://www.emdataresource.org/EMD-22389

The following previously published data sets were used

(2003) Structure of the Escherichia coli ClC Chloride channel and Fab Complex
PDB 1OTS.

https://www.rcsb.org/structure/1OTS
(2003) Structure of the Escherichia coli ClC Chloride channel E148Q mutant and Fab Complex
PDB 1OTU.

https://www.rcsb.org/structure/1OTU
1. Feng L
2. MacKinnon R
(2010) Crystal Structure of a eukaryotic CLC transporter
PDB 3ORG.

https://www.rcsb.org/structure/3ORG
(2020) Crystal structure of ClC-ec1 triple mutant (E113Q, E148Q, E203Q)
PDB 6V2J.

https://www.rcsb.org/structure/6V2J

Article and author information

Author details

Marina Schrecker

Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States

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

Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States

Competing interests
The authors declare that no competing interests exist.
Richard K Hite

Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States

For correspondence
hiter@mskcc.org

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0003-0496-0669

Funding

Searle Scholars Program

Richard K Hite

Josie Robertson Investigators Program

Richard K Hite

National Cancer Institute (accessory subunit)

Richard K Hite

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.