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- PDB-9kvz: Cryo-EM structure of SLC30A10 in the absence of Mn2+, determined ... -

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Basic information

Entry
Database: PDB / ID: 9kvz
TitleCryo-EM structure of SLC30A10 in the absence of Mn2+, determined in inward-facing conformation
ComponentsCalcium/manganese antiporter SLC30A10
KeywordsTRANSPORT PROTEIN / Manganese Transpoter / SLC30A10 / ZnT10
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.94 Å
AuthorsYang, H. / Zhang, J.K. / Shen, X.
Funding support China, 2items
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, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 15, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
B: Calcium/manganese antiporter SLC30A10
A: Calcium/manganese antiporter SLC30A10


Theoretical massNumber of molelcules
Total (without water)105,4822
Polymers105,4822
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Calcium/manganese antiporter SLC30A10 / Solute carrier family 30 member 10 / Zinc transporter 10 / ZnT-10


Mass: 52740.832 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC30A10, ZNT10, ZNT8 / Production host: Homo sapiens (human) / References: UniProt: Q6XR72
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: SLC30A10 dimer of inward-facing at APO state / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 51.22 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 225307 / Symmetry type: POINT
RefinementHighest resolution: 2.94 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0034610
ELECTRON MICROSCOPYf_angle_d0.6336252
ELECTRON MICROSCOPYf_dihedral_angle_d7.097684
ELECTRON MICROSCOPYf_chiral_restr0.04770
ELECTRON MICROSCOPYf_plane_restr0.004758

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