Cryo-EM structures of human ZnT8 in both outward- and inward-facing conformations

Abstract
Data availability
Article and author information
Metrics

Abstract

ZnT8 is a Zn²⁺/H⁺ antiporter that belongs to SLC30 family and plays an essential role in regulating Zn²⁺accumulation in the insulin secretory granules of pancreatic β cells. Dysfunction of ZnT8 is associated with both type 1 and 2 diabetes. However, the Zn²⁺/H⁺ exchange mechanism of ZnT8 remains unclear due to the lack of high-resolution structures. Here, we report the cryo-EM structures of human ZnT8 (HsZnT8) in both outward- and inward-facing conformations. HsZnT8 forms a dimeric structure with four Zn²⁺ binding sites within each subunit: a highly conserved primary site in transmembrane domain (TMD) housing the Zn²⁺ substrate; an interfacial site between TMD and C-terminal domain (CTD) that modulates the Zn²⁺ transport activity of HsZnT8; and two adjacent sites buried in the cytosolic domain and chelated by conserved residues from CTD and the His-Cys-His (HCH) motif from the N-terminal segment of the neighboring subunit. A comparison of the outward- and inward-facing structures reveals that the TMD of each HsZnT8 subunit undergoes a large structural rearrangement, allowing for alternating access to the primary Zn²⁺site during the transport cycle. Collectively, our studies provide the structural insights into the Zn²⁺/H⁺ exchange mechanism of HsZnT8.

Data availability

The Cryo-EM maps of HsZnT8 determined in three different conditions will have been deposited in the Electron Microscopy Data Bank and. The corresponding atomic coordinates will be deposited to the RCSB Protein Data Bank, with the entry ID: EMD-22285 and PDB 6XPD for the structure of HsZnT8-DM, EMD-22286 and PDB 6XPE for the structure of HsZnT8-WT in the presence of zinc, and EMD-22287 and PDB 6XPF for the structure of HsZnT8-WT in the absence of zinc. Source data files have been provided for Figure 2h and 2i.

The following previously published data sets were used

1. Lu M
2. Chai J
3. Fu D
(2009) Structural basis for the autoregulation of the zinc transporter YiiP
Electron Microscopy Data Bank, 3h90.

https://www.ebi.ac.uk/pdbe/entry/pdb/3h90
(2018) CryoEM Structure of the Zinc Transporter YiiP from helical crystals
Electron Microscopy Data Bank, 5vrf.

https://www.ebi.ac.uk/pdbe/entry/pdb/5vrf

Article and author information

Author details

Jing Xue

Department of Physiology, University of Texas Southwestern Medical Center, Dallas, United States

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

Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States

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

Department of Physiology, University of Texas Southwestern Medical Center, Dallas, United States

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

Department of Physiology, University of Texas Southwestern Medical Center, Dallas, United States

For correspondence
youxing.jiang@utsouthwestern.edu

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-1874-0504
Xiao-chen Bai

Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, United States

For correspondence
Xiaochen.Bai@UTSouthwestern.edu

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-4234-5686

Funding

National Institute of General Medical Sciences (R01GM136976)

Xiao-chen Bai

Welch Foundation (I-1944)

Xiao-chen Bai

Cancer Prevention and Research Institute of Texas (RP160082)

Xiao-chen Bai

Howard Hughes Medical Institute

Youxing Jiang

National Institute of General Medical Sciences (GM079179)

Youxing Jiang

Welch Foundation (I-1578)

Youxing Jiang

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.