8J7U

Cryo-EM structure of hZnT7-Fab complex in zinc-bound state, determined in outward-facing conformation


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.12 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Cryo-EM structures of human zinc transporter ZnT7 reveal the mechanism of Zn 2+ uptake into the Golgi apparatus.

Bui, H.B.Watanabe, S.Nomura, N.Liu, K.Uemura, T.Inoue, M.Tsutsumi, A.Fujita, H.Kinoshita, K.Kato, Y.Iwata, S.Kikkawa, M.Inaba, K.

(2023) Nat Commun 14: 4770-4770

  • DOI: https://doi.org/10.1038/s41467-023-40521-5
  • Primary Citation of Related Structures:  
    8J7T, 8J7U, 8J7V, 8J7W, 8J7X, 8J7Y, 8J80

  • PubMed Abstract: 

    Zinc ions (Zn 2+ ) are vital to most cells, with the intracellular concentrations of Zn 2+ being tightly regulated by multiple zinc transporters located at the plasma and organelle membranes. We herein present the 2.2-3.1 Å-resolution cryo-EM structures of a Golgi-localized human Zn 2+ /H + antiporter ZnT7 (hZnT7) in Zn 2+ -bound and unbound forms. Cryo-EM analyses show that hZnT7 exists as a dimer via tight interactions in both the cytosolic and transmembrane (TM) domains of two protomers, each of which contains a single Zn 2+ -binding site in its TM domain. hZnT7 undergoes a TM-helix rearrangement to create a negatively charged cytosolic cavity for Zn 2+ entry in the inward-facing conformation and widens the luminal cavity for Zn 2+ release in the outward-facing conformation. An exceptionally long cytosolic histidine-rich loop characteristic of hZnT7 binds two Zn 2+ ions, seemingly facilitating Zn 2+ recruitment to the TM metal transport pathway. These structures permit mechanisms of hZnT7-mediated Zn 2+ uptake into the Golgi to be proposed.


  • Organizational Affiliation

    Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Miyagi, 980-8577, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Zinc transporter 7A,
F [auth B]
390Homo sapiensMutation(s): 0 
Gene Names: SLC30A7ZNT7ZNTL2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NEW0 (Homo sapiens)
Explore Q8NEW0 
Go to UniProtKB:  Q8NEW0
PHAROS:  Q8NEW0
GTEx:  ENSG00000162695 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8NEW0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Heavy chain of YN7114-08 FabB [auth E],
E [auth F]
234Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Light chain of YN7114-08 Fab
C, D
218Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.12 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan18H03978
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan21H04758
Ministry of Education, Culture, Sports, Science and Technology (Japan)Japan21H05247

Revision History  (Full details and data files)

  • Version 1.0: 2023-09-20
    Type: Initial release
  • Version 1.1: 2024-11-06
    Changes: Data collection, Structure summary