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- EMDB-38475: Cryo-EM structure of human ZnT1 WT at a low PH, in the presence o... -

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Basic information

Entry
Database: EMDB / ID: EMD-38475
TitleCryo-EM structure of human ZnT1 WT at a low PH, in the presence of zinc, determined in an inward-facing conformation.
Map data
Sample
  • Complex: Zinc transporter 1
    • Protein or peptide: Proton-coupled zinc antiporter SLC30A1
  • Ligand: ZINC ION
  • Ligand: Lauryl Maltose Neopentyl Glycol
  • Ligand: CHOLESTEROL HEMISUCCINATE
KeywordsHuman ZnT1 / Zinc transpoter / Inward-facing conformation / transpost protein / TRANSPORT PROTEIN
Function / homology
Function and homology information


negative regulation of zinc ion transmembrane import / zinc export across plasma membrane / detoxification of zinc ion / detoxification of cadmium ion / Zinc efflux and compartmentalization by the SLC30 family / zinc ion import into organelle / cadmium ion transmembrane transport / zinc:proton antiporter activity / glutamatergic postsynaptic density / regulation of postsynaptic density protein 95 clustering ...negative regulation of zinc ion transmembrane import / zinc export across plasma membrane / detoxification of zinc ion / detoxification of cadmium ion / Zinc efflux and compartmentalization by the SLC30 family / zinc ion import into organelle / cadmium ion transmembrane transport / zinc:proton antiporter activity / glutamatergic postsynaptic density / regulation of postsynaptic density protein 95 clustering / zinc ion transmembrane transporter activity / zinc ion transport / zinc ion transmembrane transport / negative regulation of calcium ion import / negative regulation of neurotransmitter secretion / positive regulation of dendritic spine morphogenesis / intracellular zinc ion homeostasis / calcium ion import / postsynaptic density, intracellular component / calcium channel inhibitor activity / T-tubule / postsynaptic density membrane / cytoplasmic vesicle membrane / Schaffer collateral - CA1 synapse / intracellular calcium ion homeostasis / basolateral plasma membrane / nuclear membrane / in utero embryonic development / defense response to bacterium / dendrite / Golgi apparatus / endoplasmic reticulum / membrane / metal ion binding / 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: 3.64 Å
AuthorsQu Q / Long Y / Zhou Z
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171194 China
CitationJournal: EMBO Rep / Year: 2024
Title: Structural insights into human zinc transporter ZnT1 mediated Zn efflux.
Authors: Yonghui Long / Zhini Zhu / Zixuan Zhou / Chuanhui Yang / Yulin Chao / Yuwei Wang / Qingtong Zhou / Ming-Wei Wang / Qianhui Qu /
Abstract: Zinc transporter 1 (ZnT1), the principal carrier of cytosolic zinc to the extracellular milieu, is important for cellular zinc homeostasis and resistance to zinc toxicity. Despite recent advancements ...Zinc transporter 1 (ZnT1), the principal carrier of cytosolic zinc to the extracellular milieu, is important for cellular zinc homeostasis and resistance to zinc toxicity. Despite recent advancements in the structural characterization of various zinc transporters, the mechanism by which ZnTs-mediated Zn translocation is coupled with H or Ca remains unclear. To visualize the transport dynamics, we determined the cryo-electron microscopy (cryo-EM) structures of human ZnT1 at different functional states. ZnT1 dimerizes via extensive interactions between the cytosolic (CTD), the transmembrane (TMD), and the unique cysteine-rich extracellular (ECD) domains. At pH 7.5, both protomers adopt an outward-facing (OF) conformation, with Zn ions coordinated at the TMD binding site by distinct compositions. At pH 6.0, ZnT1 complexed with Zn exhibits various conformations [OF/OF, OF/IF (inward-facing), and IF/IF]. These conformational snapshots, together with biochemical investigation and molecular dynamic simulations, shed light on the mechanism underlying the proton-dependence of ZnT1 transport.
History
DepositionDec 27, 2023-
Header (metadata) releaseOct 30, 2024-
Map releaseOct 30, 2024-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38475.png

Downloads & links

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Map

FileDownload / File: emd_38475.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 260 pix.
= 216.32 Å		0.83 Å/pix.
x 260 pix.
= 216.32 Å		0.83 Å/pix.
x 260 pix.
= 216.32 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.32
Minimum - Maximum-1.6534103 - 2.2532413
Average (Standard dev.)-0.0015960585 (±0.060052812)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions260260260
Spacing260260260
CellA=B=C: 216.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_38475_half_map_1.map
Projections & Slices
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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_38475_half_map_2.map
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Sample components

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Entire : Zinc transporter 1

EntireName: Zinc transporter 1
Components
  • Complex: Zinc transporter 1
    • Protein or peptide: Proton-coupled zinc antiporter SLC30A1
  • Ligand: ZINC ION
  • Ligand: Lauryl Maltose Neopentyl Glycol
  • Ligand: CHOLESTEROL HEMISUCCINATE

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Supramolecule #1: Zinc transporter 1

SupramoleculeName: Zinc transporter 1 / 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: 58.055555 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 SSLSRLEEEL RRRTEGGSSD LEVLFQ

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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Macromolecule #3: Lauryl Maltose Neopentyl Glycol

MacromoleculeName: Lauryl Maltose Neopentyl Glycol / type: ligand / ID: 3 / Number of copies: 2 / Formula: AV0
Molecular weightTheoretical: 1.005188 KDa
Chemical component information

ChemComp-AV0:
Lauryl Maltose Neopentyl Glycol

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Macromolecule #4: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 4 / Number of copies: 3 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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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: 6
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 50 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 260.0 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 62.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.64 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 104963
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8xmf:
Cryo-EM structure of human ZnT1 WT at a low PH, in the presence of zinc, determined in an inward-facing conformation.

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