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- PDB-8j7t: Cryo-EM structure of hZnT7-Fab complex in zinc-unbound state, det... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8j7t | ||||||||||||
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Title | Cryo-EM structure of hZnT7-Fab complex in zinc-unbound state, determined in outward-facing conformation | ||||||||||||
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![]() | METAL TRANSPORT / zinc / proton / transporter / Golgi apparatus / metal transporter / histidine-rich loop | ||||||||||||
Function / homology | ![]() zinc ion import into Golgi lumen / Golgi cis cisterna membrane / zinc ion transmembrane transporter activity / intracellular zinc ion homeostasis / sarcoplasmic reticulum membrane / cytoplasmic vesicle / vesicle / Golgi membrane / perinuclear region of cytoplasm / Golgi apparatus ...zinc ion import into Golgi lumen / Golgi cis cisterna membrane / zinc ion transmembrane transporter activity / intracellular zinc ion homeostasis / sarcoplasmic reticulum membrane / cytoplasmic vesicle / vesicle / Golgi membrane / perinuclear region of cytoplasm / Golgi apparatus / mitochondrion / cytoplasm Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.2 Å | ||||||||||||
![]() | Han, B.B. / Inaba, K. / Watanabe, S. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM structures of human zinc transporter ZnT7 reveal the mechanism of Zn uptake into the Golgi apparatus. Authors: Han Ba Bui / Satoshi Watanabe / Norimichi Nomura / Kehong Liu / Tomoko Uemura / Michio Inoue / Akihisa Tsutsumi / Hiroyuki Fujita / Kengo Kinoshita / Yukinari Kato / So Iwata / Masahide Kikkawa / Kenji Inaba / ![]() Abstract: Zinc ions (Zn) are vital to most cells, with the intracellular concentrations of Zn being tightly regulated by multiple zinc transporters located at the plasma and organelle membranes. We herein ...Zinc ions (Zn) are vital to most cells, with the intracellular concentrations of Zn 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/H antiporter ZnT7 (hZnT7) in Zn-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-binding site in its TM domain. hZnT7 undergoes a TM-helix rearrangement to create a negatively charged cytosolic cavity for Zn entry in the inward-facing conformation and widens the luminal cavity for Zn release in the outward-facing conformation. An exceptionally long cytosolic histidine-rich loop characteristic of hZnT7 binds two Zn ions, seemingly facilitating Zn recruitment to the TM metal transport pathway. These structures permit mechanisms of hZnT7-mediated Zn uptake into the Golgi to be proposed. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 285.4 KB | Display | ![]() |
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PDB format | ![]() | 227.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 53.6 KB | Display | |
Data in CIF | ![]() | 79.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 36048MC ![]() 8j7uC ![]() 8j7vC ![]() 8j7wC ![]() 8j7xC ![]() 8j7yC ![]() 8j80C M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 43004.320 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Antibody | Mass: 24140.529 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Antibody | Mass: 24974.102 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Human ZnT7-Fab complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Microscopy | Model: JEOL CRYO ARM 300 |
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Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1700 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 115162 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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