6XPD

Cryo-EM structure of human ZnT8 double mutant - D110N and D224N, determined in outward-facing conformation


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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

Xue, J.Xie, T.Zeng, W.Jiang, Y.Bai, X.C.

(2020) Elife 9

  • DOI: https://doi.org/10.7554/eLife.58823
  • Primary Citation of Related Structures:  
    6XPD, 6XPE, 6XPF

  • PubMed Abstract: 

    ZnT8 is a Zn 2+ /H + antiporter that belongs to SLC30 family and plays an essential role in regulating Zn 2+ accumulation in the insulin secretory granules of pancreatic β cells. However, the Zn 2+ /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 Zn 2+ binding sites within each subunit: a highly conserved primary site in transmembrane domain (TMD) housing the Zn 2+ substrate; an interfacial site between TMD and C-terminal domain (CTD) that modulates the Zn 2+ 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 Zn 2+ site during the transport cycle. Collectively, our studies provide the structural insights into the Zn 2+ /H + exchange mechanism of HsZnT8.


  • Organizational Affiliation

    Howard Hughes Medical Institute and Department of Physiology, University of Texas Southwestern Medical Center, Dallas, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Zinc transporter 8A [auth B],
B [auth A]
320Homo sapiensMutation(s): 2 
Gene Names: SLC30A8ZNT8
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IWU4 (Homo sapiens)
Explore Q8IWU4 
Go to UniProtKB:  Q8IWU4
PHAROS:  Q8IWU4
GTEx:  ENSG00000164756 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IWU4
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-05
    Type: Initial release
  • Version 1.1: 2020-08-12
    Changes: Database references
  • Version 1.2: 2024-03-06
    Changes: Data collection, Database references