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Cryo-EM structures of human zinc transporter ZnT7 reveal the mechanism of Zn²⁺ uptake into the Golgi apparatus

Bui, Han Ba Watanabe, Satoshi Nomura, Norimichi Liu, Kehong Uemura, Tomoko Inoue, Michio Tsutsumi, Akihisa Fujita, Hiroyuki Kinoshita, Kengo Kato, Yukinari Iwata, So Kikkawa, Masahide Inaba, Kenji 京都大学 DOI:10.1038/s41467-023-40521-5

2023.08.08

概要

Zinc ions (Zn²⁺) are vital to most cells, with the intracellular concentrations of Zn²⁺ being tightly regulated by multiple zinc transporters located at the plasma and organelle membranes. We herein present the 2.2-3.1 Å-resolution cryo-EM structures of a Golgi-localized human Zn²⁺/H+ antiporter ZnT7 (hZnT7) in Zn²⁺-bound and unbound forms. Cryo-EM analyses show that hZnT7 exists as a dimer via tight interactions in both the cytosolic and transmembrane (TM) domains of two protomers, each of which contains a single Zn²⁺-binding site in its TM domain. hZnT7 undergoes a TM-helix rearrangement to create a negatively charged cytosolic cavity for Zn²⁺ entry in the inward-facing conformation and widens the luminal cavity for Zn²⁺ release in the outward-facing conformation. An exceptionally long cytosolic histidine-rich loop characteristic of hZnT7 binds two Zn²⁺ ions, seemingly facilitating Zn²⁺ recruitment to the TM metal transport pathway. These structures permit mechanisms of hZnT7-mediated Zn²⁺ uptake into the Golgi to be proposed.

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Acknowledgements

We thank T. Yokoyama, K. Nanatani, J. Inoue, S. Koshiba and M. Yamamoto for management of the cryo-EM facility at Tohoku University

Medical Megabank. This work was supported by funding from AMED-

Nature Communications | (2023)14:4770

https://doi.org/10.1038/s41467-023-40521-5

CREST (21gm1410006h0001) to K.I., JSPS KAKENHI to K.I. (18H03978,

21H04758 and 21H05247), Canon Medical Systems Corporation to K.K.

and K.I., and the Basis for Supporting Innovative Drug Discovery and Life

Science Research (BINDS) from the Japan Agency for Medical Research

and Development (AMED) under grant numbers JP19am0101115 (support

number: 1025), JP19am0101078 (support No. 2293), JP21am0101079

(support no. 2343) and JP22ama121038.

Author contributions

H.B.B. performed almost all experiments, structure modeling and

structure refinement. S.W. performed acquisition of cryo-EM images

with CRYO-ARM300II, image processing, structure modeling and

refinement and assisted in sample preparation. A.T. and M.K. acquired

cryo-EM images with Talos Arctica and Titan Krios G3i. N.N., K.L., T.U. and

S.I. prepared the monoclonal antibody Fab fragment recognizing hZnT7.

Y.K. provided anti-PA-tag antibody beads for purification of PA-tagged

hZnT7. M.I. prepared a stable expression cell line for hZnT7. H.F. and K.K.

provided many insights into structures and mechanisms of SLC transporters including zinc transporters to improve the manuscript. H.B.B.,

S.W. and K.I. prepared the figures and wrote the manuscript. All authors

discussed the results, critically read the manuscript, and approved the

manuscript for submission. K.I. supervised this work.

Competing interests

The authors declare no competing interests.

Additional information

Supplementary information The online version contains

supplementary material available at

https://doi.org/10.1038/s41467-023-40521-5.

Correspondence and requests for materials should be addressed to

Kenji Inaba.

Peer review information Nature Communications thanks the anonymous reviewers for their contribution to the peer review of this work. A

peer review file is available.

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