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- EMDB-61514: Cryo-EM structure of human ZnT3 -

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Basic information

Entry
Database: EMDB / ID: EMD-61514
TitleCryo-EM structure of human ZnT3
Map data
Sample
  • Complex: ZnT3
    • Protein or peptide: Probable proton-coupled zinc antiporter SLC30A3
  • Ligand: ZINC ION
  • Ligand: Lauryl Maltose Neopentyl Glycol
Keywordszinc transporter / membrane protein / ZnT / antiporter
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: 2.72 Å
AuthorsIshida H / Yo R / Zhnag Z / Shimizu T / Ohto U
Funding support Japan, 1 items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)20K16274 and 22K07131 (H.I.); 22K15046 and 24K09349 (Z.Z.); 19H00976, 22H05184, and 23H00366 (T.S.); and 19H03164 and 22H02556 [U.O.) Japan
CitationJournal: To Be Published
Title: Structural basis for the zinc transporters, ZnT3 and ZnT4
Authors: Ishida H / Yo R / Zhang Z / Shimizu T / Ohto U
History
DepositionSep 12, 2024-
Header (metadata) releaseJun 4, 2025-
Map releaseJun 4, 2025-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_61514.png

Downloads & links

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Map

FileDownload / File: emd_61514.map.gz / Format: CCP4 / Size: 103 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 300 pix.
= 249. Å		0.83 Å/pix.
x 300 pix.
= 249. Å		0.83 Å/pix.
x 300 pix.
= 249. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0424
Minimum - Maximum-0.087467 - 0.20134851
Average (Standard dev.)-0.000338483 (±0.004545887)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 249.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_61514_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_61514_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : ZnT3

EntireName: ZnT3
Components
  • Complex: ZnT3
    • Protein or peptide: Probable proton-coupled zinc antiporter SLC30A3
  • Ligand: ZINC ION
  • Ligand: Lauryl Maltose Neopentyl Glycol

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Supramolecule #1: ZnT3

SupramoleculeName: ZnT3 / 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: 43.927316 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEPSPAAGGL ETTRLVSPRD RGGAGGSLRL KSLFTEPSEP LPEESKPVEM PFHHCHRDPL PPPGLTPERL HARRQLYAAC AVCFVFMAG EVVGGYLAHS LAIMTDAAHL LADVGSMMGS LFSLWLSTRP ATRTMTFGWH RSETLGALAS VVSLWMVTGI L LYLAFVRL ...String:
MEPSPAAGGL ETTRLVSPRD RGGAGGSLRL KSLFTEPSEP LPEESKPVEM PFHHCHRDPL PPPGLTPERL HARRQLYAAC AVCFVFMAG EVVGGYLAHS LAIMTDAAHL LADVGSMMGS LFSLWLSTRP ATRTMTFGWH RSETLGALAS VVSLWMVTGI L LYLAFVRL LHSDYHIEGG AMLLTASIAV CANLLMAFVL HQAGPPHSHG SRGAEYAPLE EGPEEPLPLG NTSVRAAFVH VL GDLLQSF GVLAASILIY FKPQYKAADP ISTFLFSICA LGSTAPTLRD VLRILMEGTP RNVGFEPVRD TLLSVPGVRA THE LHLWAL TLTYHVASAH LAIDSTADPE AVLAEASSRL YSRFGFSSCT LQVEQYQPEM AQCLRCQEPP QAGSIEGRIV KDYK 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: 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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 68.0 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: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.72 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 234000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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