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- EMDB-67133: ZnT10 dimer with zinc -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-67133
TitleZnT10 dimer with zinc
Map data
Sample
  • Complex: ZnT10 dimer with zinc
    • Protein or peptide: Calcium/manganese antiporter SLC30A10
  • Ligand: ZINC ION
Keywordstransporter / METAL TRANSPORT
Function / homology
Function and homology information


manganese ion export across plasma membrane / calcium:manganese antiporter activity / detoxification of zinc ion / zinc ion import into organelle / manganese ion transport / Metal ion SLC transporters / manganese ion transmembrane transporter activity / intracellular manganese ion homeostasis / zinc ion transmembrane transporter activity / zinc ion transmembrane transport ...manganese ion export across plasma membrane / calcium:manganese antiporter activity / detoxification of zinc ion / zinc ion import into organelle / manganese ion transport / Metal ion SLC transporters / manganese ion transmembrane transporter activity / intracellular manganese ion homeostasis / zinc ion transmembrane transporter activity / zinc ion transmembrane transport / intracellular zinc ion homeostasis / metal ion transport / cellular response to angiotensin / recycling endosome / epidermal growth factor receptor signaling pathway / recycling endosome membrane / early endosome membrane / early endosome / positive regulation of ERK1 and ERK2 cascade / Golgi membrane / lysosomal membrane / Golgi apparatus / membrane / plasma membrane
Similarity search - Function
Cation efflux protein, cytoplasmic domain / Cation efflux protein, cytoplasmic domain / : / Cation efflux protein / Cation efflux transmembrane domain superfamily / Cation efflux transmembrane domain
Similarity search - Domain/homology
Calcium/manganese antiporter SLC30A10
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.15 Å
AuthorsMu H / Yang C / Feng R / Wang Y / Song D / Yu H / Chi X
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)32471304 China
CitationJournal: Biomolecules / Year: 2026
Title: Structure Basis for Chloride Recognition and Transport by Human Kidney Brain Anion Transporter (KBAT)
Authors: Wang Y / Xie T / Wu S / Wang A / Cheng W / Huang J / Yan R / Chi X
History
DepositionNov 18, 2025-
Header (metadata) releaseSep 30, 2026-
Map releaseSep 30, 2026-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_67133.png

Downloads & links

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Map

FileDownload / File: emd_67133.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 220 pix.
= 239.14 Å		1.09 Å/pix.
x 220 pix.
= 239.14 Å		1.09 Å/pix.
x 220 pix.
= 239.14 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.087 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.359
Minimum - Maximum-0.5672331 - 1.3040931
Average (Standard dev.)0.0010006902 (±0.053804446)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 239.14 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_67133_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_67133_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 : ZnT10 dimer with zinc

EntireName: ZnT10 dimer with zinc
Components
  • Complex: ZnT10 dimer with zinc
    • Protein or peptide: Calcium/manganese antiporter SLC30A10
  • Ligand: ZINC ION

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Supramolecule #1: ZnT10 dimer with zinc

SupramoleculeName: ZnT10 dimer with zinc / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Calcium/manganese antiporter SLC30A10

MacromoleculeName: Calcium/manganese antiporter SLC30A10 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 52.740832 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGRYSGKTCR LLFMLVLTVA FFVAELVSGY LGNSIALLSD SFNMLSDLIS LCVGLSAGYI ARRPTRGFSA TYGYARAEVV GALSNAVFL TALCFTIFVE AVLRLARPER IDDPELVLIV GVLGLLVNVV GLLIFQDCAA WFACCLRGRS RRLQQRQQLA E GCVPGAFG ...String:
MGRYSGKTCR LLFMLVLTVA FFVAELVSGY LGNSIALLSD SFNMLSDLIS LCVGLSAGYI ARRPTRGFSA TYGYARAEVV GALSNAVFL TALCFTIFVE AVLRLARPER IDDPELVLIV GVLGLLVNVV GLLIFQDCAA WFACCLRGRS RRLQQRQQLA E GCVPGAFG GPQGAEDPRR AADPTAPGSD SAVTLRGTSV ERKREKGATV FANVAGDSFN TQNEPEDMMK KEKKSEALNI RG VLLHVMG DALGSVVVVI TAIIFYVLPL KSEDPCNWQC YIDPSLTVLM VIIILSSAFP LIKETAAILL QMVPKGVNME ELM SKLSAV PGISSVHEVH IWELVSGKII ATLHIKYPKD RGYQDASTKI REIFHHAGIH NVTIQFENVD LKEPLEQKDL LLLC NSPCI SKGCAKQLCC PPGALPLAHV NGCAEHNGGP SLDTYGSDGL SRRDAREVAI EVSLDSCLSD HGQSLNKTQE DQCYV NRTH F

UniProtKB: Calcium/manganese antiporter SLC30A10

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS 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: SPOT SCAN / 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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 307232
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: MAXIMUM LIKELIHOOD

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