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- EMDB-60435: Cryo-EM structure of human ZnT1, in the presence of zinc, determi... -

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Basic information

Entry
Database: EMDB / ID: EMD-60435
TitleCryo-EM structure of human ZnT1, in the presence of zinc, determined in outward-facing conformation
Map data
Sample
  • Complex: Cryo-EM structure of the ZnT1 in the presence of Zinc
    • Protein or peptide: Proton-coupled zinc antiporter SLC30A1
  • Ligand: ZINC ION
KeywordsCopper uptake / Cuproptosis / ZnT family / zinc transport / TRANSPORT PROTEIN
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 / detoxification of cadmium ion / zinc ion import into organelle / zinc:proton antiporter activity / Zinc efflux and compartmentalization by the SLC30 family / cadmium ion transmembrane transport / regulation of postsynaptic density protein 95 clustering ...negative regulation of zinc ion transmembrane import / glutamatergic postsynaptic density / zinc export across plasma membrane / detoxification of zinc ion / detoxification of cadmium ion / zinc ion import into organelle / zinc:proton antiporter activity / Zinc efflux and compartmentalization by the SLC30 family / cadmium ion transmembrane transport / regulation of postsynaptic density protein 95 clustering / zinc ion transport / negative regulation of neurotransmitter secretion / zinc ion transmembrane transporter activity / negative regulation of calcium ion import / 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 / basolateral plasma membrane / nuclear 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.59 Å
AuthorsMa J / Zheng S
Funding support China, 1 items
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 6, 2024-
Header (metadata) releaseAug 21, 2024-
Map releaseAug 21, 2024-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60435.png

Downloads & links

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Map

FileDownload / File: emd_60435.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 200 pix.
= 217.4 Å		1.09 Å/pix.
x 200 pix.
= 217.4 Å		1.09 Å/pix.
x 200 pix.
= 217.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.087 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.415
Minimum - Maximum-3.4667058 - 5.2710752
Average (Standard dev.)-0.0016891587 (±0.09261673)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 217.40001 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_60435_half_map_1.map
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Half map: #2

Fileemd_60435_half_map_2.map
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Sample components

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Entire : Cryo-EM structure of the ZnT1 in the presence of Zinc

EntireName: Cryo-EM structure of the ZnT1 in the presence of Zinc
Components
  • Complex: Cryo-EM structure of the ZnT1 in the presence of Zinc
    • Protein or peptide: Proton-coupled zinc antiporter SLC30A1
  • Ligand: ZINC ION

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Supramolecule #1: Cryo-EM structure of the ZnT1 in the presence of Zinc

SupramoleculeName: Cryo-EM structure of the ZnT1 in the presence of Zinc / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Proton-coupled zinc antiporter SLC30A1

MacromoleculeName: Proton-coupled zinc antiporter SLC30A1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 55.362605 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGCWGRNRGR LLCMLALTFM FMVLEVVVSR VTSSLAMLSD SFHMLSDVLA LVVALVAERF ARRTHATQKN TFGWIRAEVM GALVNAIFL TGLCFAILLE AIERFIEPHE MQQPLVVLGV GVAGLLVNVL GLCLFHHHSG FSQDSGHGHS HGGHGHGHGL P KGPRVKST ...String:
MGCWGRNRGR LLCMLALTFM FMVLEVVVSR VTSSLAMLSD SFHMLSDVLA LVVALVAERF ARRTHATQKN TFGWIRAEVM GALVNAIFL TGLCFAILLE AIERFIEPHE MQQPLVVLGV GVAGLLVNVL GLCLFHHHSG FSQDSGHGHS HGGHGHGHGL P KGPRVKST RPGSSDINVA PGEQGPDQEE TNTLVANTSN SNGLKLDPAD PENPRSGDTV EVQVNGNLVR EPDHMELEED RA GQLNMRG VFLHVLGDAL GSVIVVVNAL VFYFSWKGCS EGDFCVNPCF PDPCKAFVEI INSTHASVYE AGPCWVLYLD PTL CVVMVC ILLYTTYPLL KESALILLQT VPKQIDIRNL IKELRNVEGV EEVHELHVWQ LAGSRIIATA HIKCEDPTSY MEVA KTIKD VFHNHGIHAT TIQPEFASVG SKSSVVPCEL ACRTQCALKQ CCGTLPQAPS GKDAEKTPAV SISCLELSNN LEKKP RRTK AENIPAVVIE IKNMPNKQPE SSL

UniProtKB: Proton-coupled zinc antiporter SLC30A1

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Macromolecule #2: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / Number of copies: 8 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.8 µm / Nominal defocus min: 1.23 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.59 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 359002
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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