8J7W | pdb_00008j7w

Cryo-EM structure of hZnT7-Fab complex in zinc state 2, determined in heterogeneous conformations- one subunit in an inward-facing zinc-bound and the other in an outward-facing zinc-bound conformation

• PDB DOI: https://doi.org/10.2210/pdb8J7W/pdb
• EM Map EMD-36051: EMDB EMDataResource

• Classification: METAL TRANSPORT
• Organism(s): Homo sapiens, Mus musculus
• Expression System: Homo sapiens, Mus musculus
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMDmpstruc


• Deposited: 2023-04-28 Released: 2023-09-20 
• Deposition Author(s): Han, B.B., Inaba, K., Watanabe, S.
• Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology (Japan)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.92 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

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

• PubMed: 37553324 
• DOI: https://doi.org/10.1038/s41467-023-40521-5
• Primary Citation 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.

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Organizational Affiliation: 
• Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Miyagi, 980-8577, Japan.
Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, 980-8577, Japan.
Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, Miyagi, 980-8578, Japan.
Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan.
Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
Advanced Research Laboratory, Canon Medical Systems Corporation, Otawara, 324-8550, Japan.
Department of System Bioinformatics, Graduate School of Information Sciences, Tohoku University, Sendai, Miyagi, 980-8579, Japan.
Department of Integrative Genomics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, 980-8573, Japan.
Graduate School of Medicine, Tohoku University, Sendai, 980-8575, Japan.
Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, Sendai, Miyagi, 980-8577, Japan. [e-mail].
Department of Molecular and Chemical Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, 980-8577, Japan. [e-mail].
Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, Miyagi, 980-8578, Japan. [e-mail].
Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan. [e-mail].
Core Research for Evolutional Science and Technology (CREST), Japan Agency for Medical Research and Development (AMED), Chiyoda-ku, Tokyo, Japan. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A2B2C2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 184.37 kDa 
• Atom Count: 11,026 
• Modeled Residue Count: 1,425 
• Deposited Residue Count: 1,684 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Zinc transporter 7	A, B	390	Homo sapiens	Mutation(s): 0  Gene Names: SLC30A7, ZNT7, ZNTL2 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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of YN7114-08 Fab	C, D	218	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of YN7114-08 Fab	E, F	234	Mus musculus	Mutation(s): 0

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.92 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-09-20 
Deposition Author(s): Han, B.B., Inaba, K., Watanabe, S.

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Funding Organization	Location	Grant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	18H03978
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	21H04758
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	21H05247

Revision History  

• Version 1.0: 2023-09-20
  Type: Initial release
  
• Version 1.1: 2024-10-16
  Changes: Data collection, Structure summary
• Version 1.2: 2025-07-02
  Changes: Data collection