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- PDB-8zsb: Cryo-EM structure of human ZnT1, in the absence of zinc, determin... -

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Basic information

Entry
Database: PDB / ID: 8zsb
TitleCryo-EM structure of human ZnT1, in the absence of zinc, determined in outward-facing conformation
ComponentsProton-coupled zinc antiporter SLC30A1
KeywordsTRANSPORT PROTEIN / Copper uptake / Cuproptosis / ZnT family
Function / homology
Function and homology information


negative regulation of zinc ion transmembrane import / glutamatergic postsynaptic density / zinc export across plasma membrane / detoxification of zinc ion / zinc ion import into organelle / detoxification of cadmium ion / zinc:proton antiporter activity / Zinc efflux and compartmentalization by the SLC30 family / cadmium ion transmembrane transport / negative regulation of calcium ion import ...negative regulation of zinc ion transmembrane import / glutamatergic postsynaptic density / zinc export across plasma membrane / detoxification of zinc ion / zinc ion import into organelle / detoxification of cadmium ion / zinc:proton antiporter activity / Zinc efflux and compartmentalization by the SLC30 family / cadmium ion transmembrane transport / negative regulation of calcium ion import / regulation of postsynaptic density protein 95 clustering / zinc ion transport / zinc ion transmembrane transporter activity / negative regulation of neurotransmitter secretion / zinc ion transmembrane transport / positive regulation of dendritic spine morphogenesis / intracellular zinc ion homeostasis / calcium ion import / postsynaptic density, intracellular component / calcium channel inhibitor activity / T-tubule / cytoplasmic vesicle membrane / postsynaptic density membrane / Schaffer collateral - CA1 synapse / intracellular calcium ion homeostasis / nuclear membrane / basolateral plasma membrane / in utero embryonic development / defense response to bacterium / Golgi membrane / dendrite / endoplasmic reticulum membrane / endoplasmic reticulum / Golgi apparatus / metal ion binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
Cation efflux protein, cytoplasmic domain superfamily / Cation efflux protein / Cation efflux transmembrane domain superfamily / Cation efflux family
Similarity search - Domain/homology
Proton-coupled zinc antiporter SLC30A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.26 Å
AuthorsMa, J. / Zheng, S.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China) China
CitationJournal: Cell Metab / Year: 2024
Title: Zinc transporter 1 functions in copper uptake and cuproptosis.
Authors: Yehua Li / Jiahao Ma / Rui Wang / Yuanhanyu Luo / Sanduo Zheng / Xiaodong Wang /
Abstract: Copper (Cu) is a co-factor for several essential metabolic enzymes. Disruption of Cu homeostasis results in genetic diseases such as Wilson's disease. Here, we show that the zinc transporter 1 (ZnT1) ...Copper (Cu) is a co-factor for several essential metabolic enzymes. Disruption of Cu homeostasis results in genetic diseases such as Wilson's disease. Here, we show that the zinc transporter 1 (ZnT1), known to export zinc (Zn) out of the cell, also mediates Cu entry into cells and is required for Cu-induced cell death, cuproptosis. Structural analysis and functional characterization indicate that Cu and Zn share the same primary binding site, allowing Zn to compete for Cu uptake. Among ZnT members, ZnT1 harbors a unique inter-subunit disulfide bond that stabilizes the outward-open conformations of both protomers to facilitate efficient Cu transport. Specific knockout of the ZnT1 gene in the intestinal epithelium caused the loss of Lgr5+ stem cells due to Cu deficiency. ZnT1, therefore, functions as a dual Zn and Cu transporter and potentially serves as a target for using Zn in the treatment of Wilson's disease caused by Cu overload.
History
DepositionJun 5, 2024Deposition site: PDBJ / Processing site: PDBC
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Proton-coupled zinc antiporter SLC30A1
B: Proton-coupled zinc antiporter SLC30A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,8564
Polymers110,7252
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Proton-coupled zinc antiporter SLC30A1 / Solute carrier family 30 member 1 / Zinc transporter 1


Mass: 55362.605 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC30A1, ZNT1 / Production host: Homo sapiens (human) / References: UniProt: Q9Y6M5
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Cryo-EM structure of the ZnT1 in the apo state / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 64000 X / Nominal defocus max: 3250 nm / Nominal defocus min: 1230 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 890

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 709780 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0024892
ELECTRON MICROSCOPYf_angle_d0.5176651
ELECTRON MICROSCOPYf_dihedral_angle_d4.295650
ELECTRON MICROSCOPYf_chiral_restr0.041797
ELECTRON MICROSCOPYf_plane_restr0.005830

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