9HRS | pdb_00009hrs

ZnT1 CTD regulation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 
    0.280 (Depositor), 0.284 (DCC) 
  • R-Value Work: 
    0.225 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 
    0.228 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Structural and functional insights of ZnT1 C-terminal domain as a regulator of zinc transport.

Ben Yosef, T.E.Kass, I.Shahar, A.Eremenko, E.Monsonego, A.Gitler, D.Moran, A.Zarivach, R.

(2025) Sci Rep 15: 26920-26920

  • DOI: https://doi.org/10.1038/s41598-025-07351-5
  • Primary Citation of Related Structures:  
    9HRS, 9IF2

  • PubMed Abstract: 

    Zinc is an essential trace element vital for cellular function, and its homeostasis is tightly regulated. ZnT1, a cation diffusion facilitator (CDF) family member, extrudes excess zinc across the mammalian plasma membrane, making it a major part of the zinc homeostasis system. While ZnT1 shares structural similarities with other CDF proteins, the role of its C-terminal domain (CTD) in zinc transport remains unclear. We used structural determination and comparative analysis, site-directed mutagenesis, and functional zinc transport assays to demonstrate that the ZnT1 CTD is a regulatory element. The regulation involves a distinct CTD conformational change upon structural, non-transported zinc binding. The observed conformational changes in the mammalian CTD are different from those observed in prokaryotic CDFs. The effects of mutating the CTD zinc-binding site on zinc transport are consistent with a hierarchical trend in the CTD regulatory role, possibly due to the importance of the CTD zinc-binding residues. This is in contrast to mutations designed to induce different prokaryotic CTD conformations that do not affect transport. Finally, we show that the unstructured extension of the CTD is dispensable, and its deletion does not affect zinc transport. Our findings establish the CTD as a key modulator of ZnT1 activity, revealing both conserved and divergent regulatory strategies across species. By elucidating ZnT1's transport regulation, this study advances our understanding of how structurally related transporters fine-tune zinc homeostasis across biological systems.


  • Organizational Affiliation
    • Department of Life Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proton-coupled zinc antiporter SLC30A1A [auth B],
B [auth A]
76Homo sapiensMutation(s): 0 
Gene Names: SLC30A1ZNT1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y6M5 (Homo sapiens)
Explore Q9Y6M5 
Go to UniProtKB:  Q9Y6M5
PHAROS:  Q9Y6M5
GTEx:  ENSG00000170385 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y6M5
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free:  0.280 (Depositor), 0.284 (DCC) 
  • R-Value Work:  0.225 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 0.228 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.595α = 90
b = 71.394β = 90
c = 67.51γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
CRANK2phasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Israel Science FoundationIsraelISF 2047/20

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-17
    Type: Initial release