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- EMDB-61516: Cryo-EM structure of human ZnT4 D150N/D281N -

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Basic information

Entry
Database: EMDB / ID: EMD-61516
TitleCryo-EM structure of human ZnT4 D150N/D281N
Map data
Sample
  • Complex: ZnT4
    • Protein or peptide: Probable proton-coupled zinc antiporter SLC30A4
Keywordszinc transporter / membrane protein / ZnT / antiporter
Function / homology
Function and homology information


zinc ion import into lysosome / zinc export across plasma membrane / zinc ion transmembrane transporter activity / zinc ion transmembrane transport / antiporter activity / response to zinc ion / response to toxic substance / late endosome membrane / late endosome / endosome membrane ...zinc ion import into lysosome / zinc export across plasma membrane / zinc ion transmembrane transporter activity / zinc ion transmembrane transport / antiporter activity / response to zinc ion / response to toxic substance / late endosome membrane / late endosome / endosome membrane / lysosomal 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 transmembrane domain
Similarity search - Domain/homology
Probable proton-coupled zinc antiporter SLC30A4
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.03 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_61516.png

Downloads & links

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Map

FileDownload / File: emd_61516.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: 0.04
Minimum - Maximum-0.091206886 - 0.19205223
Average (Standard dev.)-0.0004524273 (±0.0045422553)
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: #1

Fileemd_61516_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_61516_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 : ZnT4

EntireName: ZnT4
Components
  • Complex: ZnT4
    • Protein or peptide: Probable proton-coupled zinc antiporter SLC30A4

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Supramolecule #1: ZnT4

SupramoleculeName: ZnT4 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Probable proton-coupled zinc antiporter SLC30A4

MacromoleculeName: Probable proton-coupled zinc antiporter SLC30A4 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 49.470715 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAGSGAWKRL KSMLRKDDAP LFLNDTSAFD FSDEAGDEGL SRFNKLRVVV ADDGSEAPER PVNGAHPTLQ ADDDSLLDQD LPLTNSQLS LKVDSCDNCS KQREILKQRK VKARLTIAAV LYLLFMIGEL VGGYIANSLA IMTDALHMLT NLSAIILTLL A LWLSSKSP ...String:
MAGSGAWKRL KSMLRKDDAP LFLNDTSAFD FSDEAGDEGL SRFNKLRVVV ADDGSEAPER PVNGAHPTLQ ADDDSLLDQD LPLTNSQLS LKVDSCDNCS KQREILKQRK VKARLTIAAV LYLLFMIGEL VGGYIANSLA IMTDALHMLT NLSAIILTLL A LWLSSKSP TKRFTFGFHR LEVLSAMISV LLVYILMGFL LYEAVQRTIH MNYEINGDIM LITAAVGVAV NVIMGFLLNQ SG HRHSHSH SLPSNSPTRG SGCERNHGQD SLAVRAAFVH ALGNLVQSVG VLIAAYIIRF KPEYKIADPI CTYVFSLLVA FTT FRIIWD TVVIILEGVP SHLNVDYIKE ALMKIEDVYS VEDLNIWSLT SGKSTAIVHI QLIPGSSSKW EEVQSKANHL LLNT FGMYR CTIQLQSYRQ EVDRTCANCQ SSSPGSIEGR IVKDYKDDDD K

UniProtKB: Probable proton-coupled zinc antiporter SLC30A4

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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: 48.0 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: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 556000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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