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- EMDB-38494: Cryo-EM structure of human ZnT3, in the presence of zinc, determi... -

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Basic information

Entry
Database: EMDB / ID: EMD-38494
TitleCryo-EM structure of human ZnT3, in the presence of zinc, determined in an inward-facing conformation
Map data
Sample
  • Complex: Zinc transporter 3
    • Protein or peptide: Probable proton-coupled zinc antiporter SLC30A3
  • Ligand: ZINC ION
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: Lauryl Maltose Neopentyl Glycol
  • Ligand: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
KeywordsHuman ZnT3 / Zinc transpoter / inward- facing conformation / transport protein / transport ptotein.
Function / homology
Function and homology information


zinc ion import into synaptic vesicle / positive regulation of transport / hippocampal mossy fiber / zinc ion import into lysosome / Zinc efflux and compartmentalization by the SLC30 family / microvesicle / zinc ion transmembrane transporter activity / zinc ion transmembrane transport / antiporter activity / response to zinc ion ...zinc ion import into synaptic vesicle / positive regulation of transport / hippocampal mossy fiber / zinc ion import into lysosome / Zinc efflux and compartmentalization by the SLC30 family / microvesicle / zinc ion transmembrane transporter activity / zinc ion transmembrane transport / antiporter activity / response to zinc ion / hippocampal mossy fiber to CA3 synapse / synaptic vesicle membrane / late endosome membrane / late endosome / synaptic vesicle / neuron projection / lysosomal membrane / glutamatergic synapse / 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
Probable proton-coupled zinc antiporter SLC30A3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.14 Å
AuthorsZhu Z / Qu 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 28, 2023-
Header (metadata) releaseOct 30, 2024-
Map releaseOct 30, 2024-
UpdateNov 27, 2024-
Current statusNov 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38494.png

Downloads & links

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Map

FileDownload / File: emd_38494.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: 0.34
Minimum - Maximum-2.1523254 - 3.5440252
Average (Standard dev.)0.0008445223 (±0.08119801)
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: #1

Fileemd_38494_half_map_1.map
Projections & Slices
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Histogram (log scale)

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Half map: #2

Fileemd_38494_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Zinc transporter 3

EntireName: Zinc transporter 3
Components
  • Complex: Zinc transporter 3
    • Protein or peptide: Probable proton-coupled zinc antiporter SLC30A3
  • Ligand: ZINC ION
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • Ligand: Lauryl Maltose Neopentyl Glycol
  • Ligand: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE

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Supramolecule #1: Zinc transporter 3

SupramoleculeName: Zinc transporter 3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Probable proton-coupled zinc antiporter SLC30A3

MacromoleculeName: Probable proton-coupled zinc antiporter SLC30A3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 42.602523 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPFHHCHRDP LPPPGLTPER LHARRQLYAA CAVCFVFMAG EVVGGYLAHS LAIMTDAAHL LADVGSMMGS LFSLWLSTRP ATRTMTFGW HRSETLGALA SVVSLWMVTG ILLYLAFVRL LHSDYHIEGG AMLLTASIAV CANLLMAFVL HQAGPPHSHG S RGAEYAPL ...String:
MPFHHCHRDP LPPPGLTPER LHARRQLYAA CAVCFVFMAG EVVGGYLAHS LAIMTDAAHL LADVGSMMGS LFSLWLSTRP ATRTMTFGW HRSETLGALA SVVSLWMVTG ILLYLAFVRL LHSDYHIEGG AMLLTASIAV CANLLMAFVL HQAGPPHSHG S RGAEYAPL EEGPEEPLPL GNTSVRAAFV HVLGDLLQSF GVLAASILIY FKPQYKAADP ISTFLFSICA LGSTAPTLRD VL RILMEGT PRNVGFEPVR DTLLSVPGVR ATHELHLWAL TLTYHVASAH LAIDSTADPE AVLAEASSRL YSRFGFSSCT LQV EQYQPE MAQCLRCQEP PQASDLEVLF QGPEFWSHPQ FEKGGGSGGG SGGSAWSHPQ FEKEFDIDYK DDDDK

UniProtKB: Probable proton-coupled zinc antiporter SLC30A3

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Macromolecule #2: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / Number of copies: 6 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #3: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 3 / Number of copies: 2 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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Macromolecule #4: Lauryl Maltose Neopentyl Glycol

MacromoleculeName: Lauryl Maltose Neopentyl Glycol / type: ligand / ID: 4 / 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 #5: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-...

MacromoleculeName: (1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE
type: ligand / ID: 5 / Number of copies: 1 / Formula: A1L42
Molecular weightTheoretical: 751.023 Da
Chemical component information

ChemComp-PGT:
(1S)-2-{[{[(2R)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL STEARATE / phospholipid*YM

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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
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: 3.14 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 341267
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-8xn1:
Cryo-EM structure of human ZnT3, in the presence of zinc, determined in an inward-facing conformation

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