7Y5H | pdb_00007y5h

Cryo-EM structure of a eukaryotic ZnT8 at a low pH

• PDB DOI: https://doi.org/10.2210/pdb7Y5H/pdb
• EM Map EMD-33620: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Xenopus tropicalis
• Expression System: Komagataella pastoris
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMmpstruc


• Deposited: 2022-06-17 Released: 2022-12-14 
• Deposition Author(s): Zhang, S., Fu, C., Luo, Y., Sun, Z., Su, Z., Zhou, X.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.72 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Cryo-EM structure of a eukaryotic zinc transporter at a low pH suggests its Zn 2+ -releasing mechanism.

Zhang, S., Fu, C., Luo, Y., Xie, Q., Xu, T., Sun, Z., Su, Z., Zhou, X.

(2022) J Struct Biol 215: 107926-107926

• PubMed: 36464198 
• DOI: https://doi.org/10.1016/j.jsb.2022.107926
• Primary Citation of Related Structures:  
  7Y5G, 7Y5H


• PubMed Abstract: 
  

  Zinc transporter 8 (ZnT8) is mainly expressed in pancreatic islet β cells and is responsible for H ⁺ -coupled uptake (antiport) of Zn ²⁺ into the lumen of insulin secretory granules. Structures of human ZnT8 and its prokaryotic homolog YiiP have provided structural basis for constructing a plausible transport cycle for Zn ²⁺ . However, the mechanistic role that protons play in the transport process remains unclear. Here we present a lumen-facing cryo-EM structure of ZnT8 from Xenopus tropicalis (xtZnT8) in the presence of Zn ²⁺ at a luminal pH (5.5). Compared to a Zn ²⁺ -bound xtZnT8 structure at a cytosolic pH (7.5), the low-pH structure displays an empty transmembrane Zn ²⁺ -binding site with a disrupted coordination geometry. Combined with a Zn ²⁺ -binding assay our data suggest that protons may disrupt Zn ²⁺ coordination at the transmembrane Zn ²⁺ -binding site in the lumen-facing state, thus facilitating Zn ²⁺ release from ZnT8 into the lumen.

---

Organizational Affiliation: 
• Department of Integrated Traditional Chinese and Western Medicine, Rare Diseases Center, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China.
The State Key Laboratory of Biotherapy, Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China.
Department of Integrated Traditional Chinese and Western Medicine, Rare Diseases Center, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China. Electronic address: [e-mail].
The State Key Laboratory of Biotherapy, Department of Geriatrics and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China. Electronic address: [e-mail].
Department of Integrated Traditional Chinese and Western Medicine, Rare Diseases Center, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 83.34 kDa 
• Atom Count: 4,704 
• Modeled Residue Count: 600 
• Deposited Residue Count: 748 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Zinc transporter 8	A [auth B], B [auth A]	374	Xenopus tropicalis	Mutation(s): 0  Gene Names: slc30a8 Membrane Entity: Yes
UniProt
Find proteins for Q5XHB4 (Xenopus tropicalis) Explore Q5XHB4  Go to UniProtKB:  Q5XHB4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	C [auth B], D [auth B], E [auth A], F [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.72 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.19.1
RECONSTRUCTION	cryoSPARC	3.2

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-12-14 
Deposition Author(s): Zhang, S., Fu, C., Luo, Y., Sun, Z., Su, Z., Zhou, X.

---

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31770783

Revision History  

• Version 1.0: 2022-12-14
  Type: Initial release
  
• Version 1.1: 2022-12-21
  Changes: Database references
• Version 1.2: 2024-07-03
  Changes: Data collection, Refinement description