7Y5H

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


Experimental Data Snapshot

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

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This is version 1.1 of the entry. See complete history


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

  • 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Zinc transporter 8A [auth B],
B [auth A]
374Xenopus tropicalisMutation(s): 0 
Gene Names: slc30a8
Membrane Entity: Yes 
UniProt
Find proteins for Q5XHB4 (Xenopus tropicalis)
Explore Q5XHB4 
Go to UniProtKB:  Q5XHB4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5XHB4
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.72 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19.1
RECONSTRUCTIONcryoSPARC3.2

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31770783

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-14
    Type: Initial release
  • Version 1.1: 2022-12-21
    Changes: Database references