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- EMDB-62604: Cryo-EM structure of SLC30A10, determined in asymmetric conformat... -

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Basic information

Entry
Database: EMDB / ID: EMD-62604
TitleCryo-EM structure of SLC30A10, determined in asymmetric conformations-one subunit in an inward-facing Mn2+-bound and the other in an outward-facing Mn2+-unbound conformation
Map data
Sample
  • Complex: SLC30A10 dimer of inward-facing with manganese and outward-facing without manganese
    • Protein or peptide: Calcium/manganese antiporter SLC30A10
  • Ligand: MANGANESE (II) ION
KeywordsManganese Transpoter / SLC30A10 / ZnT10 / TRANSPORT PROTEIN
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 / Metal ion SLC transporters / manganese ion transport / intracellular manganese ion homeostasis / manganese ion transmembrane transporter activity / 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 / Metal ion SLC transporters / manganese ion transport / intracellular manganese ion homeostasis / manganese ion transmembrane transporter activity / zinc ion transmembrane transporter activity / zinc ion transmembrane transport / intracellular zinc ion homeostasis / 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 / Golgi apparatus / membrane / plasma membrane
Similarity search - Function
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: 3.34 Å
AuthorsYang H / Zhang JK / Shen X
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171216 China
Ministry of Science and Technology (MoST, China)STI2030-Major Projects 2022ZD0212600 China
CitationJournal: Nat Commun / Year: 2025
Title: Molecular mechanisms of SLC30A10-mediated manganese transport.
Authors: Xurui Shen / Jinlun Kylian Zhang / Peixin Sun / Huiwen Zhong / Rui He / Shiliang Wang / Xiaojun Guo / Hanting Yang /
Abstract: Manganese ion (Mn²⁺) is crucial for various physiological processes, yet excessive levels disrupt cellular homeostasis and impair the function of multiple organelles. The transporter SLC30A10 ...Manganese ion (Mn²⁺) is crucial for various physiological processes, yet excessive levels disrupt cellular homeostasis and impair the function of multiple organelles. The transporter SLC30A10 plays a pivotal role in Mn²⁺ homeostasis by exporting Mn²⁺ from cells, preventing toxic effects. Mutations in the SLC30A10 gene result in Mn²⁺ accumulation and lead to disorders such as hypermanganesemia with dystonia 1 (HMNDYT1). Despite its physiological significance, the structural basis underlying Mn²⁺ binding and the detailed transport mechanisms of SLC30A10 remain unknown. Here, we present diverse conformations of high-resolution cryo-electron microscopy (cryo-EM) structures that reveal a Mn²⁺-binding site in SLC30A10, setting it apart from other SLC30 family transporters. Furthermore, we show that the HMNDYT1-associated D40A mutation interrupts Mn²⁺ binding and transport, identifying D40 as a potential therapeutic target. These findings provide structural insights into Mn²⁺ transport mechanisms mediated by SLC30A10, advancing our understanding of Mn²⁺ binding and potential targets for future therapeutic exploration.
History
DepositionDec 5, 2024-
Header (metadata) releaseOct 15, 2025-
Map releaseOct 15, 2025-
UpdateOct 15, 2025-
Current statusOct 15, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62604.png

Downloads & links

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Map

FileDownload / File: emd_62604.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 256 pix.
= 238.592 Å		0.93 Å/pix.
x 256 pix.
= 238.592 Å		0.93 Å/pix.
x 256 pix.
= 238.592 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.932 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.22681594 - 0.30925515
Average (Standard dev.)0.00008126225 (±0.0085267145)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 238.592 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_62604_additional_1.map
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Half map: #1

Fileemd_62604_half_map_1.map
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Half map: #2

Fileemd_62604_half_map_2.map
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Sample components

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Entire : SLC30A10 dimer of inward-facing with manganese and outward-facing...

EntireName: SLC30A10 dimer of inward-facing with manganese and outward-facing without manganese
Components
  • Complex: SLC30A10 dimer of inward-facing with manganese and outward-facing without manganese
    • Protein or peptide: Calcium/manganese antiporter SLC30A10
  • Ligand: MANGANESE (II) ION

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Supramolecule #1: SLC30A10 dimer of inward-facing with manganese and outward-facing...

SupramoleculeName: SLC30A10 dimer of inward-facing with manganese and outward-facing without manganese
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: MANGANESE (II) ION

MacromoleculeName: MANGANESE (II) ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: MN
Molecular weightTheoretical: 54.938 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: 6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.91 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.34 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 273127
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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