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- PDB-6xpd: Cryo-EM structure of human ZnT8 double mutant - D110N and D224N, ... -
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Basic information
Entry | Database: PDB / ID: 6xpd | ||||||
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Title | Cryo-EM structure of human ZnT8 double mutant - D110N and D224N, determined in outward-facing conformation | ||||||
![]() | Zinc transporter 8 | ||||||
![]() | TRANSPORT PROTEIN / ZnT8 / zinc transporter | ||||||
Function / homology | ![]() Zinc efflux and compartmentalization by the SLC30 family / zinc ion import into organelle / zinc:proton antiporter activity / zinc ion import across plasma membrane / insulin processing / zinc ion transmembrane transporter activity / zinc ion transport / zinc ion transmembrane transport / regulation of vesicle-mediated transport / intracellular zinc ion homeostasis ...Zinc efflux and compartmentalization by the SLC30 family / zinc ion import into organelle / zinc:proton antiporter activity / zinc ion import across plasma membrane / insulin processing / zinc ion transmembrane transporter activity / zinc ion transport / zinc ion transmembrane transport / regulation of vesicle-mediated transport / intracellular zinc ion homeostasis / insulin secretion / transport vesicle membrane / response to zinc ion / Insulin processing / response to type II interferon / response to glucose / response to interleukin-1 / secretory granule membrane / secretory granule / positive regulation of insulin secretion / cytoplasmic vesicle / Golgi membrane / intracellular membrane-bounded organelle / protein homodimerization activity / zinc ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å | ||||||
![]() | Bai, X.C. / Xue, J. / Jiang, Y.X. | ||||||
![]() | ![]() Title: Cryo-EM structures of human ZnT8 in both outward- and inward-facing conformations. Authors: Jing Xue / Tian Xie / Weizhong Zeng / Youxing Jiang / Xiao-Chen Bai / ![]() Abstract: ZnT8 is a Zn/H antiporter that belongs to SLC30 family and plays an essential role in regulating Zn accumulation in the insulin secretory granules of pancreatic β cells. However, the Zn/H exchange ...ZnT8 is a Zn/H antiporter that belongs to SLC30 family and plays an essential role in regulating Zn accumulation in the insulin secretory granules of pancreatic β cells. However, the Zn/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 binding sites within each subunit: a highly conserved primary site in transmembrane domain (TMD) housing the Zn substrate; an interfacial site between TMD and C-terminal domain (CTD) that modulates the Zn 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 site during the transport cycle. Collectively, our studies provide the structural insights into the Zn/H exchange mechanism of HsZnT8. | ||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 114.5 KB | Display | ![]() |
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PDB format | ![]() | 87.9 KB | Display | ![]() |
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-Validation report
Summary document | ![]() | 901.3 KB | Display | ![]() |
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Full document | ![]() | 912.1 KB | Display | |
Data in XML | ![]() | 23.1 KB | Display | |
Data in CIF | ![]() | 32.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 22285MC ![]() 6xpeC ![]() 6xpfC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 35086.160 Da / Num. of mol.: 2 / Mutation: D110N, D224N Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Chemical | ChemComp-ZN / Has ligand of interest | Y | |
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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 Znt8 double mutant - D110N and D224N / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Value: 0.035 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 7.4 |
Specimen | Conc.: 4 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
EM imaging optics | Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV / Phase plate: VOLTA PHASE PLATE |
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Processing
Software | Name: PHENIX / Version: 1.17.1_3660: / Classification: refinement | |||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | |||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 55851 / Symmetry type: POINT | |||||||||||||||||||||||||||
Refine LS restraints |
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